The trainers, believed to number about 20, were working with Pakistan's frontier constabulary - a paramilitary force on the front line of the fight against the Taliban and al-Qaeda.
The Ministry of Defence said it was due to "security concerns".
But it added that the withdrawal was temporary.
Strained relationsA spokeswoman said: "The UK has been asked to withdraw some of its training support teams on a temporary basis by the Pakistan government in response to security concerns.
"We are providing training support at the invitation of the Pakistan government and welcome their advice on these matters.
"The training teams will continue their own training and will be ready to redeploy at the first possible opportunity."
The United States has already had to bring home more than 100 military trainers.
The BBC's Orla Guerin, in Islamabad, said the ?15m training programme looks like another casualty of the strained relations between Pakistan and its Western allies since US special forces killed Osama Bin Laden on 2 May.
Quick returnPakistan is still smarting from the raid which it views as an attack on its sovereignty, she said.
It is understood some of the trainers remain in the region, so they could make a quick return.
The MoD said it was "not as if the relationship has come to a sour end".
Another British training programme covering improvised explosive devices has not been affected.
British military trainers have been training and assisting Pakistan's Frontier Corps in military operations as part of a three-year programme which started in 2010.
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