diff --git a/sql/src/main/java/org/apache/druid/sql/calcite/schema/DruidSchema.java b/sql/src/main/java/org/apache/druid/sql/calcite/schema/DruidSchema.java
index 3efbd8d0074e..2929229b4c59 100644
--- a/sql/src/main/java/org/apache/druid/sql/calcite/schema/DruidSchema.java
+++ b/sql/src/main/java/org/apache/druid/sql/calcite/schema/DruidSchema.java
@@ -19,6 +19,7 @@
 
 package org.apache.druid.sql.calcite.schema;
 
+import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Preconditions;
 import com.google.common.base.Predicates;
 import com.google.common.collect.FluentIterable;
@@ -402,7 +403,8 @@ private void addSegment(final DruidServerMetadata server, final DataSegment segm
     }
   }
 
-  private void removeSegment(final DataSegment segment)
+  @VisibleForTesting
+  protected void removeSegment(final DataSegment segment)
   {
     synchronized (lock) {
       log.debug("Segment[%s] is gone.", segment.getId());
@@ -450,7 +452,8 @@ private void removeServerSegment(final DruidServerMetadata server, final DataSeg
    * Attempt to refresh "segmentSignatures" for a set of segments. Returns the set of segments actually refreshed,
    * which may be a subset of the asked-for set.
    */
-  private Set<DataSegment> refreshSegments(final Set<DataSegment> segments) throws IOException
+  @VisibleForTesting
+  protected Set<DataSegment> refreshSegments(final Set<DataSegment> segments) throws IOException
   {
     final Set<DataSegment> retVal = new HashSet<>();
 
@@ -506,15 +509,26 @@ private Set<DataSegment> refreshSegmentsForDataSource(final String dataSource, f
             log.debug("Segment[%s] has signature[%s].", segment.getId(), rowSignature);
             final Map<DataSegment, SegmentMetadataHolder> dataSourceSegments =
                 segmentMetadataInfo.get(segment.getDataSource());
-            SegmentMetadataHolder holder = dataSourceSegments.get(segment);
-            SegmentMetadataHolder updatedHolder = SegmentMetadataHolder
-                .from(holder)
-                .withRowSignature(rowSignature)
-                .withNumRows(analysis.getNumRows())
-                .build();
-            dataSourceSegments.put(segment, updatedHolder);
-            setSegmentSignature(segment, updatedHolder);
-            retVal.add(segment);
+            if (dataSourceSegments == null) {
+              log.warn("No segment map found with datasource[%s], skipping refresh", segment.getDataSource());
+            } else {
+              SegmentMetadataHolder holder = dataSourceSegments.get(segment);
+              if (holder == null) {
+                log.warn(
+                    "No segment[%s] found, skipping refresh",
+                    segment.getId()
+                );
+              } else {
+                SegmentMetadataHolder updatedHolder = SegmentMetadataHolder
+                    .from(holder)
+                    .withRowSignature(rowSignature)
+                    .withNumRows(analysis.getNumRows())
+                    .build();
+                dataSourceSegments.put(segment, updatedHolder);
+                setSegmentSignature(segment, updatedHolder);
+                retVal.add(segment);
+              }
+            }
           }
         }
 
@@ -628,7 +642,7 @@ private static RowSignature analysisToRowSignature(final SegmentAnalysis analysi
     return rowSignatureBuilder.build();
   }
 
-  public Map<DataSegment, SegmentMetadataHolder> getSegmentMetadata()
+  Map<DataSegment, SegmentMetadataHolder> getSegmentMetadata()
   {
     final Map<DataSegment, SegmentMetadataHolder> segmentMetadata = new HashMap<>();
     synchronized (lock) {
diff --git a/sql/src/test/java/org/apache/druid/sql/calcite/schema/DruidSchemaTest.java b/sql/src/test/java/org/apache/druid/sql/calcite/schema/DruidSchemaTest.java
index 1b4e00819bb6..30b99e59ab44 100644
--- a/sql/src/test/java/org/apache/druid/sql/calcite/schema/DruidSchemaTest.java
+++ b/sql/src/test/java/org/apache/druid/sql/calcite/schema/DruidSchemaTest.java
@@ -63,6 +63,7 @@
 import java.io.IOException;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 public class DruidSchemaTest extends CalciteTestBase
 {
@@ -237,4 +238,38 @@ public void testGetTableMapFoo2()
     Assert.assertEquals("m1", fields.get(2).getName());
     Assert.assertEquals(SqlTypeName.BIGINT, fields.get(2).getType().getSqlTypeName());
   }
+
+  @Test
+  public void testNullDatasource() throws IOException
+  {
+    Map<DataSegment, SegmentMetadataHolder> segmentMetadatas = schema.getSegmentMetadata();
+    Set<DataSegment> segments = segmentMetadatas.keySet();
+    Assert.assertEquals(segments.size(), 3);
+    // segments contains two segments with datasource "foo" and one with datasource "foo2"
+    // let's remove the only segment with datasource "foo2"
+    final DataSegment segmentToRemove = segments.stream().filter(segment -> segment.getDataSource().equals("foo2")).findFirst().orElse(null);
+    Assert.assertFalse(segmentToRemove == null);
+    schema.removeSegment(segmentToRemove);
+    schema.refreshSegments(segments); // can cause NPE without dataSourceSegments null check in DruidSchema#refreshSegmentsForDataSource
+    segmentMetadatas = schema.getSegmentMetadata();
+    segments = segmentMetadatas.keySet();
+    Assert.assertEquals(segments.size(), 2);
+  }
+
+  @Test
+  public void testNullSegmentMetadataHolder() throws IOException
+  {
+    Map<DataSegment, SegmentMetadataHolder> segmentMetadatas = schema.getSegmentMetadata();
+    Set<DataSegment> segments = segmentMetadatas.keySet();
+    Assert.assertEquals(segments.size(), 3);
+    //remove one of the segments with datasource "foo"
+    final DataSegment segmentToRemove = segments.stream().filter(segment -> segment.getDataSource().equals("foo")).findFirst().orElse(null);
+    Assert.assertFalse(segmentToRemove == null);
+    schema.removeSegment(segmentToRemove);
+    schema.refreshSegments(segments); // can cause NPE without holder null check in SegmentMetadataHolder#from
+    segmentMetadatas = schema.getSegmentMetadata();
+    segments = segmentMetadatas.keySet();
+    Assert.assertEquals(segments.size(), 2);
+  }
+
 }