It is better to wait until an enemy missile has gotten to the most inner circle of your radar. Then, press B button to drop chaffs and flares to ward off the incoming missile. Do not stop pressing B until the missile lock warning goes off.

In addition, fly closer to the ground (below 500 feet) when you have a lot of enemy fighters in the air. The incoming enemy missiles are typically coming down (if you are flying low) and impact upon the ground. Be sure to press B button until the missile lock warning goes off.