Major Jon Swift, who is currently serving in Afghanistan, said Britain is sustaining higher casualties than official figures suggest and condemned the operation as "politically" driven.
"The scale of casualties has not been properly reported and shows no sign of reducing, he said in comments initially posted on a regimental website, but later withdrawn.
"Political and not military imperatives are being followed in the campaign."
But the Ministry of Defence says criticism of the Royal Air Force in Afghanistan is not shared by the majority of soldiers, where British forces are struggling against a fiercer-than-expected insurgency.
A ministry spokesman insists all serious casualties are recorded.
"We publish our casualty figures, and they cover all serious injuries," he said.
"We're not going to go and capture (figures) for everybody who gets a cut."
According to the latest ministry figures, 125 people were evacuated from Afghanistan for medical reasons between January and the end of July 2006, including four categorised as very seriously injured.
RAF ‘utterly useless’
Meanwhile, emails written by an unidentified major condemned the RAF as "utterly, utterly useless" and underlined that more soldiers and equipment were desperately needed.
The Ministry of Defence described the emails as "unfortunate" but downplayed their significance.
"They do not reflect the view of the vast majority of soldiers about the Harrier Force in Afghanistan, which has consistently performed brilliantly in defending coalition forces," said a spokesman.
"It must be remembered that this is the opinion of only one man. The general view is very different."
Britain took over command of NATO forces in the volatile south of Afghanistan in May, and has faced fiercer-than-anticipated resistance from Taliban insurgents.
A total of 33 British troops have died since then, compared to a total of 40 since NATO moved into Afghanistan in 2001 in the wake of the September 11 terror attacks in the United States.