diff --git a/extensions-core/multi-stage-query/src/main/java/org/apache/druid/msq/input/table/TableInputSpecSlicer.java b/extensions-core/multi-stage-query/src/main/java/org/apache/druid/msq/input/table/TableInputSpecSlicer.java
index be27543d5e2..37a97d33be5 100644
--- a/extensions-core/multi-stage-query/src/main/java/org/apache/druid/msq/input/table/TableInputSpecSlicer.java
+++ b/extensions-core/multi-stage-query/src/main/java/org/apache/druid/msq/input/table/TableInputSpecSlicer.java
@@ -103,6 +103,7 @@ public class TableInputSpecSlicer implements InputSpecSlicer
                         .flatMap(
                             holder ->
                                 StreamSupport.stream(holder.getObject().spliterator(), false)
+                                             .filter(chunk -> !chunk.getObject().isTombstone())
                                              .map(
                                                  chunk ->
                                                      new DataSegmentWithInterval(
diff --git a/extensions-core/multi-stage-query/src/test/java/org/apache/druid/msq/input/table/TableInputSpecSlicerTest.java b/extensions-core/multi-stage-query/src/test/java/org/apache/druid/msq/input/table/TableInputSpecSlicerTest.java
index c411404b9cf..dbcb3646e88 100644
--- a/extensions-core/multi-stage-query/src/test/java/org/apache/druid/msq/input/table/TableInputSpecSlicerTest.java
+++ b/extensions-core/multi-stage-query/src/test/java/org/apache/druid/msq/input/table/TableInputSpecSlicerTest.java
@@ -29,6 +29,7 @@ import org.apache.druid.testing.InitializedNullHandlingTest;
 import org.apache.druid.timeline.DataSegment;
 import org.apache.druid.timeline.SegmentTimeline;
 import org.apache.druid.timeline.partition.DimensionRangeShardSpec;
+import org.apache.druid.timeline.partition.TombstoneShardSpec;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
@@ -79,13 +80,25 @@ public class TableInputSpecSlicerTest extends InitializedNullHandlingTest
       BYTES_PER_SEGMENT
   );
 
+  private static final DataSegment SEGMENT3 = new DataSegment(
+      DATASOURCE,
+      Intervals.of("2001/2002"),
+      "1",
+      Collections.emptyMap(),
+      Collections.emptyList(),
+      Collections.emptyList(),
+      TombstoneShardSpec.INSTANCE,
+      null,
+      null,
+      BYTES_PER_SEGMENT
+  );
   private SegmentTimeline timeline;
   private TableInputSpecSlicer slicer;
 
   @Before
   public void setUp()
   {
-    timeline = SegmentTimeline.forSegments(ImmutableList.of(SEGMENT1, SEGMENT2));
+    timeline = SegmentTimeline.forSegments(ImmutableList.of(SEGMENT1, SEGMENT2, SEGMENT3));
     DataSegmentTimelineView timelineView = (dataSource, intervals) -> {
       if (DATASOURCE.equals(dataSource)) {
         return Optional.of(timeline);