The soldiers from the 2nd Battalion of the Parachute Regiment - 2 Para - were on a routine foot patrol near the British forward operating base Gibraltar in the Helmand River Valley when they encountered Taleban fighters.
They called in air support from the Army's Apache helicopter, which successfully fired on a Taleban position.
But then in the confusion of what the MoD termed a "rapidly-changing situation", it fired again on another position, which the crew believed was held by the enemy.
An investigation is now under way into the incident. There was no public statement from 2 Para's headquarters in Colchester.
Major Charles Heyman says it's a 'miracle' there are not more friendly fire incidents
The BBC's Alastair Leithead in Kabul said air support had a difficult job when Taleban positions were possibly less than 100 metres away from British troops.
He said the tree-lined terrain with high compound walls and deep irrigation ditches presented further difficulties.
Retired General Sir Jack Deverell said soldiers were aware of the risk of "friendly fire" from air support.
But he added: "If I was a soldier out there I would rather have an effective air cover and run the relatively small risk of being injured by my own support than be injured by the Taleban. The threat from the Taleban is far greater."
He said he would be concerned if an attempt to increase safety checks made the system more bureaucratic.
"It could end up with more soldiers being killed because suppression fire is not close enough to protect them."
Charles Heyman, director of defence suppliers Armed Forces, said there was technology to differentiate between friend and foe.
Forward operating base Gibraltar is in the Musa Qala region
However, he said: "It is possible that the Taleban and the British soldiers were very, very close together.
"When you've got eyeball to eyeball, the technology is not going to help you as much as you hoped."
The incident is the first reported occurrence in Afghanistan of "friendly fire" involving only UK troops, although allied forces have previously hit each other's troops during the conflict.
In August last year, three soldiers from 1st Battalion The Royal Anglian Regiment were killed when US fighter planes dropped a 500lb (225kg) bomb on them.
In December 2006, marine Jonathan Wigley died in an apparent attack by the US in Helmand province.
In April 2002, an American F-16 fighter jet dropped a laser-guided 500lb (225kg) bomb near Kandahar, accidentally killing four Canadian soldiers and injuring eight others.
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