The email, from a major serving in the Sangin area of northern Helmand province in southern Afghanistan, described the Royal Air Force as "utterly, utterly useless" and underlined that more soldiers and equipment were needed "desperately," Britain's Sky News reported.
The Guardian newspaper said the email was sent by Major James Loden of 3 Para, who was awarded the Bronze Star medal in 2004 by the US military for his services in support of Operation Enduring Freedom in Afghanistan.
Major Loden heavily criticises Harrier Force, the British air force in Afghanistan, for failing to support ground troops and describes one incident where a Harrier fighter bomber dropped phosphorus rockets near British soldiers.
"A female Harrier pilot couldn't identify the target, fired two phosphorus 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," the email said.
The officer also wrote of his concerns for two junior soldiers who, in a recent firefight, "looked very frightened and slow to react". He said that many of his men were exhausted and had, at times, been reduced to tears.
A British ministry of defence spokesman said that the email gave "a moving and at times humbling account of fighting in a part of Helmand province" but described the officer's comments as unfortunate.
"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," he said in a statement.
"It must be remembered that this is the opinion of only one man. The general view is very different."
General Sir Richard Dannatt, the chief of the general staff, issued a strong defence of the air force.
"The way the RAF has performed in support of our operations in Afghanistan has been exceptional. Irresponsible comments, based on a snapshot, are regrettable," Dannatt said.
"We're not going to go and capture [figures] for everybody who gets a cut"
Ministry of Defence spokesman
"Following my recent visit, which happened after the incident described in the emails, the men of the battlegroup left me in no doubt as to the value of the RAF's support to their operations.
Also on Friday, Britain denied that that casualty figures in Afghanistan are being under-reported, as claimed by a company commander in the Royal Regiment of Fusiliers.
Major Jon Swift said "the scale of casualties has not been properly reported and shows no sign of reducing" in comments posted on a regimental website but later withdrawn. He also condemned the operation as "politically" driven.
"Political and not military imperatives are being followed in the campaign," he said.
The ministry of defence spokesman insisted that all serious casualties were recorded.
"We publish our casualty figures, and they cover all serious injuries," he said, adding: "We're not going to go and capture [figures] for everybody who gets a cut."
More than 5,000 British troops are serving in Afghanistan as part of a 20,000-strong Nato force attempting to provide security to help reconstruction and economic development efforts.