The helicopters are used primarily to move troops and kit
Helicopters being sent to Afghanistan will be able to perform "the full range of military tasks" despite claims they lack protection, the MoD has insisted.
Reports in the Daily Telegraph claimed six Merlins - due to go to Helmand in December - did not have Kevlar armour.
The paper quotes senior RAF sources as warning this could prevent the craft's use in missions against the Taliban.
Defence chiefs say the Merlins are fitted with ballistic protection and are being modified ahead of deployment.
A Ministry of Defence (MoD) spokesman said: "The Merlin is one of our best protected helicopters and we are absolutely satisfied that it will be well protected against threats in Afghanistan.
"The fleet has already successfully flown thousands of missions over Iraq, often in the face of significant danger.
"Notwithstanding Merlin's success in Iraq, we are now spending an additional £45m improving its protection.
"When deployed to Afghanistan the Merlins will be ready to perform the full range of military tasks required, including combat missions and ferrying troops into battle."
Independent aerospace analyst Andrew Brookes, from the International Institute for Strategic Studies, said he could find no evidence of pilots or commanding officers expressing concern.
"These helicopters are the same that have been flying in Iraq for some years - perfectly successfully, perfectly securely - in operational conditions."
Describing the crafts' armour as "very, very good", Mr Brookes said: "These are modern helicopters, top of the range. They aren't clapped out. They have got wonderful kit."
Transporting personnel and equipment by air reduces the risk of attack from roadside bombs, which prey on the need for coalition forces to use slow-moving convoys of heavy vehicles to replenish units.
Pilots had told the Telegraph they had called for the Merlin Mk3 helicopters, which will be used to move troops and kit around Helmand, to be upgraded at a cost of around £100,000 each.
However, they claimed their requests had been ignored.
"We are going to send aircraft out to Afghanistan that are lacking in the required protection," a Merlin fleet source told the Telegraph.
"It will be the same as driving a Snatch Land Rover along a road full of mines. I don't want people to come back strapped into their seats with bullet holes in them."
BBC diplomatic correspondent James Robbins said he understood the problem was not primarily a question of the cost, but instead that factories could not fit all the required protection in time.
The MoD considered it better to get extra helicopters to Afghanistan quickly and then allow commanders to decide on the balance of risk of how to use them, he added.
Defence Secretary Bob Ainsworth said last week he was "busting a gut" to get more helicopters out to Afghanistan following suggestions by some military leaders and politicians that there were not enough out there to support British troops.
The chief of the defence staff, Sir Jock Stirrup, said deploying more of the craft would prevent casualties. And Foreign Office minister Lord Malloch Brown said there "definitely" were not enough helicopters, before rowing back on his comments.