There were several aspects to reducing friendly fire during aircraft attacks on carrier groups. It was a frequent problem throughout the war, and could not easily be avoided.

Anti-aircraft gunners that could recognise friendly aircraft were less likely to shoot them down. This was not 100% reliable, as nervy or jumpy gunners could easily make mistakes. Crews that had recently been attacked, or who were not expecting friendly aircraft, were likely to fire before properly checking the identity of their target. This was a frequent problem for the RN in the early part of the war, when cooperation with the RAF was lacking. To make recognition natural, AA gunners were given intensive training in it, training that was frequently refreshed. This training used a combination of aircraft models and silhouettes to familiarise seamen with friendly and enemy aircraft from a variety of angles. Sometimes, gun crews would be accompanied by aircrew who weren't flying, who were more experienced in spotting friendly aircraft. Recognition could be eased through the paint schemes given to aircraft. Different countries painted their aircraft different colours, and had different identification roundels. To avoid confusion with the Japanese roundel, the British and Americans would remove the red elements from their roundels (in the British case, only for aircraft serving in the Pacific). These could be fairly subtle differences, so more obtrusive paint schemes could be used. The British had some successes during Operation Pedestal, by painting the tails and wingtips of their fighters yellow. More well-known are the 'invasion stripes', the black and white striped painted on the wings and fuselage of Allied aircraft during the Normandy landings. In these cases, the AA gunners could be instructed not to fire on aircraft painted in these ways. These measures were successful, but could only be used for a limited time, to prevent the enemy taking advantage of the pattern.

The risk of friendly fire could also be controlled by controlling how friendly aircraft operated. Fighters typically operated as the outer layer of a task force's air defences. It was common for them to stay outside the effective range of the task force's guns. They could engage any target outside that range, but turned away from attacks on aircraft that moved into the gun's range. Similarly, it was common to enforce a minimum ceiling on the CAP. Aircraft below this ceiling could be assumed to be hostile and fired on by the guns. CAP aircraft would have to drop below this level to land on the carrier to refuel and rearm; to prevent the gunners firing on them, they would have to approach the carrier along a defined corridor, usually from astern of the carrier. There might also be a recognition signal involved; British escort carriers on the Arctic convoy runs sometimes used lowered landing gear as a signal that an approaching aircraft was friendly.

Radar offered another way to identify friendly aircraft. In the interwar period, the British spent some times developing Identification Friend and Foe (IFF) systems. These had a circuit that amplified and re-sent friendly radar signals, creating a larger blob on the radar display. Later models had a system that, when 'interrogated' by a radio signal, broadcasted a bright radio signal. IFF systems were not typically fitted to gun directors, so gun crews had to wait for the central AIO/CIC (in the RN and USN respectively) to interrogate a target and pass its identity to them. This removed the possibility of friendly fire, but slowed down the reaction time for AA fire. IFF also had several inherent flaws. An aircraft that wasn't fitted with it would automatically be identified as hostile. The early versions were only compatible with one particular radar; if the ship didn't have that radar, then the aircraft would similarly be seen as hostile. IFF systems could also give away the position of a task force or air squadron, through the radio emissions associated with it. There was the ever-present worry that the enemy might work out how to mimic IFF signals, or how to send the interrogator signal - the former would allow their aircraft to be seen as friendly, the latter would make it much easier to find friendly aircraft. These issues limited the use of IFF, though it was still a great help.