|The RAF are "utterly, utterly useless" in protecting troops on the ground in Afghanistan, a major with the main UK battle group said in a leaked e-mail.
Major James Loden of 3 Para, based in the north of the southern province of Helmand, said more troops and helicopters were desperately needed.
There had been "plenty of tears" following casualties in the intense fighting with the Taleban, he added.
The MoD said the RAF played a "critical role" in supporting ground troops.
The ministry confirmed the contents of the e-mail as accurate.
The "tears" Maj Loden refers to were "not tears of exhaustion or frustration", a spokesman said.
"This is a reflection of the fact these men are under daily attack and sadly there are often daily casualties."
Describing Maj Loden's e-mail as "moving" and "humbling", the spokesman said it "reflects both how intense the fighting can occasionally be, and the enormous courage, dedication and skill of the British troops" in Helmand.
Some were "working to the limits of endurance, but their morale is high and they are winning the fight", he added.
Maj Loden's comments about the RAF "do not reflect the view of the vast majority of soldiers", the spokesman said.
It had "performed brilliantly in defending coalition forces", he added.
But Maj Loden's e-mail gives an example of the RAF's failure to provide air support.
"... Harrier pilot 'couldn't identify the target', fired two phosphorous rockets that just missed our own compound so that we thought they were incoming RPGs [rocket-propelled grenades], and then strafed our perimeter missing the enemy by 200 metres," it says.
BBC defence correspondent Paul Wood said Maj Loden's comments reflected what officers were saying privately, but their tone and emphasis were at odds with the MoD's official statements.
Other Parachute Regiment officers had told him they prefer to call in American A-10 Tankbusters for air support when under fire because of what they see as the RAF's ineffectiveness, he added.
However, in a statement released by the MoD, 3 Para operations officer in Afghanistan Capt Matt Taylor said the RAF had "played a critical part in ensuring the security of the lads on the ground".
"They could not have asked for better support during some very difficult times," he added.
British spokesman in Southern Afghanistan Lt Col Dave Reynolds added the RAF was an "enormously effective", "invaluable" and "absolutely essential part of the operations in Afghanistan".
Liberal Democrat defence spokesman Nick Harvey called on the government to "provide an urgent statement" in response to Maj Loden's "disturbing comments".
His e-mail showed "the need for a reassessment of the full range of capabilities required to accomplish the Nato mission" in Afghanistan, Mr Harvey added.
"As our troops face increasing violence, we need to see a clear and achievable strategy and an honest assessment of the challenges ahead."
The e-mail, which has been sent to British Army head Sir Richard Dannatt, comes a day after another British commander in Afghanistan said the Army there was sustaining higher casualties than official figures suggested.
Writing in the Fusiliers' newsletter, Major John Swift said some had argued many casualties had been treated in the field and, therefore, had been omitted from the official statistics for wounded in action.
Casualty numbers were very significant and showed no signs of reducing, he added.
Maj Swift also said political rather than military imperatives were driving the operation.
He was referring to the Afghan government's demand for British troops to move to isolated fire bases in northern Helmand where they are now under siege by the Taleban.