diff --git a/Tools/autotest/common.py b/Tools/autotest/common.py
index a41d3ebb52..10348dfbcd 100644
--- a/Tools/autotest/common.py
+++ b/Tools/autotest/common.py
@@ -5026,7 +5026,8 @@ Also, ignores heartbeats not from our target system'''
         if reset_needed:
             self.reset_SITL_commandline()
 
-        self.clear_mission_using_mavproxy()
+        if not self.is_tracker(): # FIXME - more to the point, fix Tracker's mission handling
+            self.clear_mission(mavutil.mavlink.MAV_MISSION_TYPE_ALL)
 
         tee.close()