diff --git a/tools/functional-tester/etcd-tester/cluster.go b/tools/functional-tester/etcd-tester/cluster.go
index d12c754e0..36a8ff4ca 100644
--- a/tools/functional-tester/etcd-tester/cluster.go
+++ b/tools/functional-tester/etcd-tester/cluster.go
@@ -322,6 +322,11 @@ func (c *cluster) compactKV(rev int64) error {
 		conn *grpc.ClientConn
 		err  error
 	)
+
+	if rev <= 0 {
+		return nil
+	}
+
 	for _, u := range c.GRPCURLs {
 		conn, err = grpc.Dial(u, grpc.WithInsecure(), grpc.WithTimeout(5*time.Second))
 		if err != nil {
@@ -329,7 +334,7 @@ func (c *cluster) compactKV(rev int64) error {
 		}
 		kvc := pb.NewKVClient(conn)
 		ctx, cancel := context.WithTimeout(context.Background(), 5*time.Second)
-		_, err = kvc.Compact(ctx, &pb.CompactionRequest{Revision: rev})
+		_, err = kvc.Compact(ctx, &pb.CompactionRequest{Revision: rev, Physical: true})
 		cancel()
 		conn.Close()
 		if err == nil {
@@ -338,3 +343,33 @@ func (c *cluster) compactKV(rev int64) error {
 	}
 	return err
 }
+
+func (c *cluster) checkCompact(rev int64) error {
+	if rev == 0 {
+		return nil
+	}
+	for _, u := range c.GRPCURLs {
+		cli, err := clientv3.New(clientv3.Config{
+			Endpoints:   []string{u},
+			DialTimeout: 5 * time.Second,
+		})
+		if err != nil {
+			return err
+		}
+
+		ctx, cancel := context.WithTimeout(context.Background(), 5*time.Second)
+		wch := cli.Watch(ctx, "\x00", clientv3.WithFromKey(), clientv3.WithRev(rev-1))
+		wr, ok := <-wch
+		cancel()
+
+		cli.Close()
+
+		if !ok {
+			return fmt.Errorf("watch channel terminated")
+		}
+		if wr.CompactRevision != rev {
+			return fmt.Errorf("got compact revision %v, wanted %v", wr.CompactRevision, rev)
+		}
+	}
+	return nil
+}
diff --git a/tools/functional-tester/etcd-tester/tester.go b/tools/functional-tester/etcd-tester/tester.go
index 2284724f9..79d916798 100644
--- a/tools/functional-tester/etcd-tester/tester.go
+++ b/tools/functional-tester/etcd-tester/tester.go
@@ -149,8 +149,15 @@ func (tt *tester) runLoop() {
 		}
 		plog.Printf("[round#%d] compacted storage", i)
 
-		// TODO: make sure compaction is finished
-		time.Sleep(30 * time.Second)
+		plog.Printf("[round#%d] check compaction at %d", i, revToCompact)
+		if err := tt.cluster.checkCompact(revToCompact); err != nil {
+			plog.Printf("[round#%d] checkCompact error (%v)", i, err)
+			if err := tt.cleanup(i, 0); err != nil {
+				plog.Printf("[round#%d] cleanup error: %v", i, err)
+				return
+			}
+		}
+		plog.Printf("[round#%d] confirmed compaction at %d", i, revToCompact)
 	}
 }