diff --git a/cmd/frostfs-node/tree.go b/cmd/frostfs-node/tree.go
index 1f73b795..175748ac 100644
--- a/cmd/frostfs-node/tree.go
+++ b/cmd/frostfs-node/tree.go
@@ -31,6 +31,10 @@ func (c cnrSource) Get(id cid.ID) (*container.Container, error) {
 	return c.src.Get(id)
 }
 
+func (c cnrSource) DeletionInfo(cid cid.ID) (*container.DelInfo, error) {
+	return c.cli.DeletionInfo(cid)
+}
+
 func (c cnrSource) List() ([]cid.ID, error) {
 	return c.cli.ContainersOf(nil)
 }
diff --git a/internal/logs/logs.go b/internal/logs/logs.go
index 6c261785..3f0a3f56 100644
--- a/internal/logs/logs.go
+++ b/internal/logs/logs.go
@@ -70,6 +70,7 @@ const (
 	TreeContainerTreesHaveBeenSynced                                        = "container trees have been synced"
 	TreeCouldNotQueryTreesForSynchronization                                = "could not query trees for synchronization"
 	TreeRemovingRedundantTrees                                              = "removing redundant trees..."
+	TreeCouldNotCheckIfContainerExisted                                     = "could not check if the container ever existed"
 	TreeCouldNotRemoveRedundantTree                                         = "could not remove redundant tree"
 	TreeCouldNotCalculateContainerNodes                                     = "could not calculate container nodes"
 	TreeFailedToApplyReplicatedOperation                                    = "failed to apply replicated operation"
diff --git a/pkg/services/tree/options.go b/pkg/services/tree/options.go
index a6e23c62..043e12cb 100644
--- a/pkg/services/tree/options.go
+++ b/pkg/services/tree/options.go
@@ -14,6 +14,9 @@ import (
 
 type ContainerSource interface {
 	container.Source
+
+	DeletionInfo(cid.ID) (*container.DelInfo, error)
+
 	// List must return list of all the containers in the FrostFS network
 	// at the moment of a call and any error that does not allow fetching
 	// container information.
diff --git a/pkg/services/tree/signature_test.go b/pkg/services/tree/signature_test.go
index 482c1615..9d4776ba 100644
--- a/pkg/services/tree/signature_test.go
+++ b/pkg/services/tree/signature_test.go
@@ -53,6 +53,10 @@ func (s dummyContainerSource) Get(id cid.ID) (*containercore.Container, error) {
 	return cnt, nil
 }
 
+func (s dummyContainerSource) DeletionInfo(id cid.ID) (*containercore.DelInfo, error) {
+	return &containercore.DelInfo{}, nil
+}
+
 type dummyEACLSource map[string]*containercore.EACL
 
 func (s dummyEACLSource) GetEACL(id cid.ID) (*containercore.EACL, error) {
diff --git a/pkg/services/tree/sync.go b/pkg/services/tree/sync.go
index e44e8dbb..62a127c6 100644
--- a/pkg/services/tree/sync.go
+++ b/pkg/services/tree/sync.go
@@ -18,6 +18,7 @@ import (
 	metrics "git.frostfs.info/TrueCloudLab/frostfs-observability/metrics/grpc"
 	tracing "git.frostfs.info/TrueCloudLab/frostfs-observability/tracing"
 	tracing_grpc "git.frostfs.info/TrueCloudLab/frostfs-observability/tracing/grpc"
+	apistatus "git.frostfs.info/TrueCloudLab/frostfs-sdk-go/client/status"
 	cid "git.frostfs.info/TrueCloudLab/frostfs-sdk-go/container/id"
 	netmapSDK "git.frostfs.info/TrueCloudLab/frostfs-sdk-go/netmap"
 	"github.com/panjf2000/ants/v2"
@@ -440,6 +441,18 @@ func (s *Service) syncContainers(ctx context.Context, cnrs []cid.ID) {
 	wg.Wait()
 }
 
+func (s *Service) containerEverExisted(cid cid.ID) (bool, error) {
+	_, err := s.cnrSource.DeletionInfo(cid)
+	if err == nil {
+		return true, nil
+	}
+	var errContainerNotFound *apistatus.ContainerNotFound
+	if errors.As(err, &errContainerNotFound) {
+		return false, nil
+	}
+	return false, err
+}
+
 func (s *Service) removeContainers(ctx context.Context, newContainers map[cid.ID]struct{}) {
 	ctx, span := tracing.StartSpanFromContext(ctx, "TreeService.removeContainers")
 	defer span.End()
@@ -452,7 +465,15 @@ func (s *Service) removeContainers(ctx context.Context, newContainers map[cid.ID
 		if _, ok := newContainers[cnr]; ok {
 			continue
 		}
-		removed = append(removed, cnr)
+
+		existed, err := s.containerEverExisted(cnr)
+		if err != nil {
+			s.log.Error(logs.TreeCouldNotCheckIfContainerExisted,
+				zap.Stringer("cid", cnr),
+				zap.Error(err))
+		} else if existed {
+			removed = append(removed, cnr)
+		}
 	}
 	for i := range removed {
 		delete(s.cnrMap, removed[i])