diff --git a/cli/util/uploader.go b/cli/util/uploader.go
index 520b04c7b..8ef315ab2 100644
--- a/cli/util/uploader.go
+++ b/cli/util/uploader.go
@@ -354,115 +354,193 @@ func uploadIndexFiles(ctx *cli.Context, p *pool.Pool, containerID cid.ID, accoun
 	}
 
 	var (
-		errCh                 = make(chan error)
-		buffer                = make([]byte, indexFileSize*oidSize)
-		oidCh                 = make(chan oid.ID, indexFileSize)
-		oidFetcherToProcessor = make(chan struct{}, indexFileSize)
-
+		buffer   = make([]byte, indexFileSize*oidSize)
+		doneCh   = make(chan struct{})
+		errCh    = make(chan error)
 		emptyOid = make([]byte, oidSize)
 	)
-	defer close(oidCh)
-	for range maxParallelSearches {
-		go func() {
-			for id := range oidCh {
-				var obj *object.Object
-				errRetr := retry(func() error {
-					var errGetHead error
-					obj, errGetHead = p.ObjectHead(context.Background(), containerID, id, signer, client.PrmObjectHead{})
-					return errGetHead
-				})
-				if errRetr != nil {
+
+	go func() {
+		defer close(doneCh)
+
+		// Main processing loop for each index file.
+		for i := existingIndexCount; i < expectedIndexCount; i++ {
+			// Start block parsing goroutines.
+			var (
+				// processedIndices is a mapping from position in buffer to the block index.
+				processedIndices sync.Map
+				wg               sync.WaitGroup
+				oidCh            = make(chan oid.ID, 2*maxParallelSearches)
+			)
+			wg.Add(maxParallelSearches)
+			for range maxParallelSearches {
+				go func() {
+					defer wg.Done()
+					for id := range oidCh {
+						var obj *object.Object
+						errRetr := retry(func() error {
+							var errGetHead error
+							obj, errGetHead = p.ObjectHead(context.Background(), containerID, id, signer, client.PrmObjectHead{})
+							return errGetHead
+						})
+						if errRetr != nil {
+							select {
+							case errCh <- fmt.Errorf("failed to fetch object %s: %w", id.String(), errRetr):
+							default:
+							}
+							return
+						}
+						blockIndex, err := getBlockIndex(obj, blockAttributeKey)
+						if err != nil {
+							select {
+							case errCh <- fmt.Errorf("failed to get block index from object %s: %w", id.String(), err):
+							default:
+							}
+							return
+						}
+						pos := uint(blockIndex) % indexFileSize
+						if _, ok := processedIndices.LoadOrStore(pos, blockIndex); !ok {
+							id.Encode(buffer[pos*oidSize:])
+						}
+					}
+				}()
+			}
+
+			// Search for blocks within the index file range.
+			startIndex := i * indexFileSize
+			endIndex := startIndex + indexFileSize
+			objIDs := searchObjects(ctx.Context, p, containerID, account, blockAttributeKey, startIndex, endIndex, maxParallelSearches, errCh)
+			for id := range objIDs {
+				oidCh <- id
+			}
+			close(oidCh)
+			wg.Wait()
+			fmt.Fprintf(ctx.App.Writer, "Index file %d generated, checking for the missing blocks...\n", i)
+
+			// Check if there are empty OIDs in the generated index file. This may happen
+			// if searchObjects has returned not all blocks within the requested range, ref.
+			// #3645. In this case, retry the search for every missing object.
+			var count int
+
+			for idx := range indexFileSize {
+				if _, ok := processedIndices.Load(idx); !ok {
+					count++
+					objIDs = searchObjects(ctx.Context, p, containerID, account, blockAttributeKey, i*indexFileSize+idx, i*indexFileSize+idx+1, 1, errCh)
+					// Block object duplicates are allowed, we're OK with the first found result.
+					id, ok := <-objIDs
+					for range objIDs {
+					}
+					if !ok {
+						select {
+						case errCh <- fmt.Errorf("block %d is missing from the storage", i*indexFileSize+idx):
+						default:
+						}
+						return
+					}
+					processedIndices.Store(idx, id)
+					id.Encode(buffer[idx*oidSize:])
+				}
+			}
+			fmt.Fprintf(ctx.App.Writer, "%d missing block(s) processed for index file %d, uploading index file...\n", count, i)
+
+			// Check if there are empty OIDs in the generated index file. If it happens at
+			// this stage, then there's a bug in the code.
+			for k := 0; k < len(buffer); k += oidSize {
+				if slices.Compare(buffer[k:k+oidSize], emptyOid) == 0 {
 					select {
-					case errCh <- fmt.Errorf("failed to fetch object %s: %w", id.String(), errRetr):
+					case errCh <- fmt.Errorf("empty OID found in index file %d at position %d (block index %d)", i, k/oidSize, i*indexFileSize+uint(k/oidSize)):
 					default:
 					}
 					return
 				}
-				blockIndex, err := getBlockIndex(obj, blockAttributeKey)
-				if err != nil {
-					select {
-					case errCh <- fmt.Errorf("failed to get block index from object %s: %w", id.String(), err):
-					default:
-					}
-					return
-				}
-				offset := (uint(blockIndex) % indexFileSize) * oidSize
-				id.Encode(buffer[offset:])
-				oidFetcherToProcessor <- struct{}{}
 			}
-		}()
-	}
 
-	for i := existingIndexCount; i < expectedIndexCount; i++ {
-		startIndex := i * indexFileSize
-		endIndex := startIndex + indexFileSize
-		go func() {
-			for j := int(startIndex); j < int(endIndex); j += searchBatchSize {
-				remaining := int(endIndex) - j
-				end := j + min(searchBatchSize, remaining)
-
-				prm = client.PrmObjectSearch{}
-				filters = object.NewSearchFilters()
-				filters.AddFilter(blockAttributeKey, fmt.Sprintf("%d", j), object.MatchNumGE)
-				filters.AddFilter(blockAttributeKey, fmt.Sprintf("%d", end), object.MatchNumLT)
-				prm.SetFilters(filters)
-				var objIDs []oid.ID
-				err := retry(func() error {
-					var errSearchIndex error
-					objIDs, errSearchIndex = neofs.ObjectSearch(ctx.Context, p, account.PrivateKey(), containerID.String(), prm)
-					return errSearchIndex
-				})
-
-				if err != nil {
-					select {
-					case errCh <- fmt.Errorf("failed to search for objects from %d to %d for index file %d: %w", j, end, i, err):
-					default:
-					}
-					return
-				}
-
-				for _, id := range objIDs {
-					oidCh <- id
-				}
+			// Upload index file.
+			attrs := []object.Attribute{
+				*object.NewAttribute(attributeKey, strconv.Itoa(int(i))),
+				*object.NewAttribute("IndexSize", strconv.Itoa(int(indexFileSize))),
 			}
-		}()
-
-		var completed int
-	waitLoop:
-		for {
-			select {
-			case err := <-errCh:
-				return err
-			case <-oidFetcherToProcessor:
-				completed++
-				if completed == int(indexFileSize) {
-					break waitLoop
+			err := retry(func() error {
+				return uploadObj(ctx.Context, p, signer, account.PrivateKey().GetScriptHash(), containerID, buffer, attrs, homomorphicHashingDisabled)
+			})
+			if err != nil {
+				select {
+				case errCh <- fmt.Errorf("failed to upload index file %d: %w", i, err):
+				default:
 				}
+				return
 			}
+			fmt.Fprintf(ctx.App.Writer, "Uploaded index file %d\n", i)
+			clear(buffer)
 		}
-		// Check if there are empty OIDs in the generated index file. If it happens at
-		// this stage, then there's a bug in the code.
-		for k := 0; k < len(buffer); k += oidSize {
-			if slices.Compare(buffer[k:k+oidSize], emptyOid) == 0 {
-				return fmt.Errorf("empty OID found in index file %d at position %d (block index %d)", i, k/oidSize, i+uint(k/oidSize))
-			}
-		}
-		attrs := []object.Attribute{
-			*object.NewAttribute(attributeKey, strconv.Itoa(int(i))),
-			*object.NewAttribute("IndexSize", strconv.Itoa(int(indexFileSize))),
-		}
-		err := retry(func() error {
-			return uploadObj(ctx.Context, p, signer, account.PrivateKey().GetScriptHash(), containerID, buffer, attrs, homomorphicHashingDisabled)
-		})
-		if err != nil {
-			return fmt.Errorf("failed to upload index file %d: %w", i, err)
-		}
-		fmt.Fprintf(ctx.App.Writer, "Uploaded index file %d\n", i)
+	}()
+
+	select {
+	case err := <-errCh:
+		return err
+	case <-doneCh:
 	}
 
 	return nil
 }
 
+// searchObjects searches in parallel for objects with attribute GE startIndex and LT
+// endIndex. It returns a buffered channel of resulting object IDs and closes it once
+// OID search is finished. Errors are sent to errCh in a non-blocking way.
+func searchObjects(ctx context.Context, p *pool.Pool, containerID cid.ID, account *wallet.Account, blockAttributeKey string, startIndex, endIndex uint, maxParallelSearches int, errCh chan error) chan oid.ID {
+	var res = make(chan oid.ID, 2*searchBatchSize)
+	go func() {
+		var wg sync.WaitGroup
+		defer close(res)
+
+		for i := int(startIndex); i < int(endIndex); i += searchBatchSize * maxParallelSearches {
+			for j := range maxParallelSearches {
+				start := i + j*searchBatchSize
+				end := start + searchBatchSize
+
+				if start >= int(endIndex) {
+					break
+				}
+				if end > int(endIndex) {
+					end = int(endIndex)
+				}
+
+				wg.Add(1)
+				go func(start, end int) {
+					defer wg.Done()
+
+					prm := client.PrmObjectSearch{}
+					filters := object.NewSearchFilters()
+					filters.AddFilter(blockAttributeKey, fmt.Sprintf("%d", start), object.MatchNumGE)
+					filters.AddFilter(blockAttributeKey, fmt.Sprintf("%d", end), object.MatchNumLT)
+					prm.SetFilters(filters)
+
+					var objIDs []oid.ID
+					err := retry(func() error {
+						var errBlockSearch error
+						objIDs, errBlockSearch = neofs.ObjectSearch(ctx, p, account.PrivateKey(), containerID.String(), prm)
+						return errBlockSearch
+					})
+					if err != nil {
+						select {
+						case errCh <- fmt.Errorf("failed to search for block(s) from %d to %d: %w", start, end, err):
+						default:
+						}
+						return
+					}
+
+					for _, id := range objIDs {
+						res <- id
+					}
+				}(start, end)
+			}
+			wg.Wait()
+		}
+	}()
+
+	return res
+}
+
 // uploadObj uploads object to the container using provided settings.
 func uploadObj(ctx context.Context, p *pool.Pool, signer user.Signer, owner util.Uint160, containerID cid.ID, objData []byte, attrs []object.Attribute, homomorphicHashingDisabled bool) error {
 	var (