The graphic images were leaked online 19 months after they are thought to have been taken following a deadly Taliban attack on Camp Bastion, the main British base in Afghanistan.
Two men from the RAF Regiment - the service's ground-fighting force - from the RAF base in Moray, have been removed from frontline duties after the pictures were posted on the Live Leak website.
In the images, a man in military fatigues is pictured smiling as he crouches and makes a thumbs-up gesture to the camera beside the bloodstained body of a man in combat gear.
The Ministry of Defence military police investigation was launched after the pictures were published.
An RAF spokeswoman said: "Inappropriate actions will not be tolerated in the Armed Forces. The RAF is treating this incident extremely seriously and has launched a military police investigation. As this incident is subject to an ongoing investigation it would be inappropriate to comment further at this time."
The images were purportedly taken at the base in the wake of the attack on September 14, 2012, by insurgents who targeted Prince Harry, then stationed at the HQ with the Army Air Corps. Two soldiers were killed, dozens of others injured and military equipment, including fighter jets, destroyed.
The 51 Squadron RAF Regiment, which is based in Moray, was involved in defending the base.
The base, which is north-west of Lashkar Gah, the capital of Helmand Province, is home to 28,000 personnel.
The events of September 14 were dubbed the "Battle of Bastion".
US Marines Squadron Commander Lieutenant Colonel Chris Raible, who was carrying only his service pistol, and Sergeant Bradley Atwell were killed and a number of British personnel were injured.
Six US Harrier jets were destroyed by the insurgents, who used rocket-propelled grenades and explosives.
The photographs appear to have been taken at night after the battle was over and also show the burnt-out remains of jets.
The attack was staged by a group of 19 insurgents dressed in US military fatigues who infiltrated the outer perimeter of Camp Bastion before splitting into three groups.
One group attacked a team of American military mechanics who were in the area, while the other two spread out into the base.
Members of 51 Squadron RAF Regiment, who were on the opposite side of the compound when the attack began, arrived 13 minutes after the alarm was raised.
According to official accounts, it took a combined force of ground troops and Apache helicopters four hours to flush out all the insurgents, 18 of whom were killed while one was captured.
It is not known if Prince Harry, who was in Afghanistan on duty as a helicopter pilot, was involved in the battle.
Last month a report by MPs said British commanders had to "bear a degree of responsibility" for failing to prevent the 2012 raid.
News of the investigation came on the day the Duke of York took the salute and 300 people lined the streets of Elgin at a homecoming parade for troops from RAF Lossiemouth. The 130 men and women from 5 Force Protection Wing returned from a tour of duty last week.
There have been previous cases of abuse by British soldiers.
Royal Marine Sergeant Alexander Blackman, from Taunton, Somerset, is serving 10 years in prison for murder after being filmed shooting dead a wounded Afghan fighter.