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The figures show out of a fleet of 40 Chinook transporters, only 17 are "fit for purpose", while 20 out of 60 new Merlin work properly and only 25 Apache attack helicopters are functioning - almost a third of the total.
Liam Fox, the shadow defence secretary, said the shortage was sure to impact on capabilities in Afghanistan and Iraq.
"When I visited troops in Helmand Province, in November, it became clear there was a shortage of Apaches and Chinooks to support troops on the ground," he added.
Col Bob Stewart, the former British commander in Bosnia, said the lack of basic equipment "translates into greater casualties".
"If you cannot move people by air it means they have to travel by road which leads to a proportionate increase in the dangers faced," he added.
The MoD said commanders in Iraq and Afghanistan had enough helicopters to do "key tasks" although "with more they could do more".