diff --git a/Orange/widgets/visualize/owscatterplot.py b/Orange/widgets/visualize/owscatterplot.py
index 5867777172d..f222791b8e6 100644
--- a/Orange/widgets/visualize/owscatterplot.py
+++ b/Orange/widgets/visualize/owscatterplot.py
@@ -294,6 +294,7 @@ def reset_graph_data(self, *_):
         self.update_graph()
 
     def set_data(self, data):
+        self.clear_messages()
         self.Information.sampled_sql.clear()
         self.__timer.stop()
         self.sampling.setVisible(False)
diff --git a/Orange/widgets/visualize/tests/test_owscatterplot.py b/Orange/widgets/visualize/tests/test_owscatterplot.py
index 08c59933b3e..91b0b7fb62c 100644
--- a/Orange/widgets/visualize/tests/test_owscatterplot.py
+++ b/Orange/widgets/visualize/tests/test_owscatterplot.py
@@ -81,3 +81,13 @@ def test_optional_combos(self):
     def _select_data(self):
         self.widget.graph.select_by_rectangle(QRectF(4, 3, 3, 1))
         return self.widget.graph.get_selection()
+
+    def test_error_message(self):
+        """Check if error message appears and then disappears when
+        data is removed from input"""
+        data = self.data.copy()
+        data.X[:, 0] = np.nan
+        self.send_signal("Data", data)
+        self.assertTrue(self.widget.Warning.missing_coords.is_shown())
+        self.send_signal("Data", None)
+        self.assertFalse(self.widget.Warning.missing_coords.is_shown())