diff --git a/EKF/covariance.cpp b/EKF/covariance.cpp
index dd2a8dfa0b..f592dc941b 100644
--- a/EKF/covariance.cpp
+++ b/EKF/covariance.cpp
@@ -91,21 +91,16 @@ void Ekf::initialiseCovariance()
 	P[15][15] = P[13][13];
 
 	// variances for optional states
-	// these state variances are set to zero until the states are required, then they must be initialised
 
-	// earth magnetic field
-	P[16][16] = 0.0f;
-	P[17][17] = 0.0f;
-	P[18][18] = 0.0f;
-
-	// body magnetic field
-	P[19][19] = 0.0f;
-	P[20][20] = 0.0f;
-	P[21][21] = 0.0f;
+	// earth frame and body frame magnetic field
+	// set to observation variance
+	for (uint8_t index=16; index <= 21; index ++) {
+		P[index][index] = sq(_params.mag_noise);
+	}
 
 	// wind
-	P[22][22] = 0.0f;
-	P[23][23] = 0.0f;
+	P[22][22] = 1.0f;
+	P[23][23] = 1.0f;
 
 }