diff --git a/Tools/autotest/arducopter.py b/Tools/autotest/arducopter.py
index 7b44ef6162..ce15b45947 100644
--- a/Tools/autotest/arducopter.py
+++ b/Tools/autotest/arducopter.py
@@ -2753,6 +2753,13 @@ class AutoTestCopter(AutoTest):
         self.set_parameter("GPS_TYPE", 0)
         self.reboot_sitl()
         self.change_mode('STABILIZE')
+        self.wait_ekf_flags((mavutil.mavlink.ESTIMATOR_ATTITUDE |
+                             mavutil.mavlink.ESTIMATOR_VELOCITY_VERT |
+                             mavutil.mavlink.ESTIMATOR_POS_VERT_ABS |
+                             mavutil.mavlink.ESTIMATOR_CONST_POS_MODE |
+                             mavutil.mavlink.ESTIMATOR_PRED_POS_HORIZ_REL),
+                            0,
+                            timeout=120)
         self.arm_vehicle()
         self.mavproxy.send("mode LOITER\n")
         self.mavproxy.expect("requires position")
diff --git a/Tools/autotest/common.py b/Tools/autotest/common.py
index 5b73e28704..ec77299fbe 100644
--- a/Tools/autotest/common.py
+++ b/Tools/autotest/common.py
@@ -1664,7 +1664,6 @@ class AutoTest(ABC):
         if (int(self.get_parameter('AHRS_EKF_TYPE')) == 10):
             return True
 
-        tstart = self.get_sim_time()
         # all of these must be set for arming to happen:
         required_value = (mavutil.mavlink.EKF_ATTITUDE |
                           mavutil.mavlink.ESTIMATOR_VELOCITY_HORIZ |
@@ -1679,9 +1678,12 @@ class AutoTest(ABC):
                                mavutil.mavlink.ESTIMATOR_POS_VERT_ABS |
                                mavutil.mavlink.ESTIMATOR_PRED_POS_HORIZ_ABS)
             error_bits |= mavutil.mavlink.ESTIMATOR_GPS_GLITCH
+        self.wait_ekf_flags(required_value, error_bits, timeout=timeout)
 
+    def wait_ekf_flags(self, required_value, error_bits, timeout=30):
         self.progress("Waiting for EKF value %u" % required_value)
         last_print_time = 0
+        tstart = self.get_sim_time()
         while timeout is None or self.get_sim_time_cached() < tstart + timeout:
             m = self.mav.recv_match(type='EKF_STATUS_REPORT', blocking=True)
             current = m.flags