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The government has acknowledged that the Foreign Office budget had been hit by the falling value of the pound.
But junior foreign office minister Chris Bryant insisted that spending on counter-terrorism programmes was increasing.
Answering an urgent question in the Commons on 21 January 2010, Mr Bryant said the percentage of that sum being spent in Pakistan had also risen.
His statement came after Foreign Office Minister Baroness Kinnock of Holyhead disclosed on Wednesday that FCO programmes to tackle terrorism and radicalisation in Pakistan had been cut due to the falling value of sterling.
Lady Kinnock was speaking at Lords questions, soon after the prime minister had told the Commons that the "crucible of terrorism" on the Afghan-Pakistan border remained the "number one security threat to the West".
Shadow Foreign Office minister David Lidington demanded that ministers should "come clean" about the scale of the cutbacks.
He said it was "appalling" to see the spectacle of Mr Brown talking about the fight against terrorism, while Lady Kinnock was outlining the impact of exchange rate problems on the counter-terrorism programme.
Mr Lidington claimed that an internal FCO memorandum from last December has also warned of cuts in posts after the general election, adding: "As ever the difficult decisions are postponed."