Raza Gilani insisted that Osama bin Laden was not in Pakistan and that his security forces had been "extremely successful" in tackling terrorists within its borders.
His comments came after Mr Brown demanded at the weekend that Pakistan did more to find and "take out" bin Laden and his deputy Ayman Zawahiri.
The Prime Minister struck a more conciliatory note today at a joint press conference with Mr Gilani in Downing Street.
After talks, Mr Brown announced that the two countries were stepping up efforts to tackle extremism and would improve intelligence-sharing.
But Mr Gilani made clear that he did not feel that Pakistan was to blame for the failure to apprehend bin Laden eight years on from 9/11.
"Pakistan is fighting the war on terrorism and we have a good intelligence and defence cooperation with the United States," he said.
When questioned about Mr Brown's previous remarks, he suggested that his security forces had not had "actionable information" on bin Laden.
"I doubt the information which you are giving is correct because I don't think Osama bin Laden is in Pakistan," he said.
Mr Gilani also rejected Mr Brown's claim that three-quarters of terror plots against the UK originated in Pakistan.
"I don't agree with this information because we are fighting this war on terrorism," Mr Gilani said.
"Yes there have been Uzbeks, there have been Arabs, there have been Talibans from Afghanistan.... but we have been very successful and we are extremely successful."
He added: "Most of them, they are not in Pakistan, they might be in Afghanistan.
"I think we are extremely successful in handling the situation."
At the weekend, Mr Brown made little attempt to hide his frustration at Pakistan's failure to track down the men responsible for 9/11.
Today, he said the UK was working with Pakistan to improve anti-terrorism efforts.
"I was talking today about the greater security co-operation we are planning between our two countries," he said.
"I think, over the next period of time, we will strengthen the security co-operation between our two countries."
He agreed that operations in Waziristan and the Swat Valley in Pakistan had "yielded great results".
But he repeated: "We have said, from the basis of our security figures, that three-quarters of terrorist plots that have happened in Britain have links to Pakistan."
Pakistani journalists expressed frustration with Mr Brown's comments, repeatedly challenging him as to what intelligence the UK had provided to their country on bin Laden's location.
Mr Brown said: "As far as what information we have on al Qaida, we will do everything to share it with our allies and that is what we continue to do.
"I think what's happened over the last few months is that all of us have agreed we need to do more to fight terrorism wherever it arises."
He went on: "What Prime Minister Gilani is also saying is that Pakistan has made its decisions to allocate more troops, first in the Swat Valley, then in Waziristan, to take on the terrorist threat in their own country.
"So we have seen, on both sides of the borders, a determination on the part of everyone concerned to take on terrorism within these borders and that is a welcome sign that all of us are working together on a common good."
The Prime Minister acknowledged the "huge sacrifices" made by Pakistan in the fight against terrorism and announced £50 million in new funding for its border regions with Afghanistan.
He said: "I think it's important that the Prime Minister has signalled, as he has done in recent months, the real importance that Pakistan attaches to dealing with these problems and I can assure him of the UK's full support in this matter.
"This is your fight, but it's also Britain's fight."
Mr Brown's spokesman said later that the Prime Minister believed the al Qa'ida leadership was in Waziristan on the "best evidence we have".
"That's his view, that is where they are likely to be," he added, acknowledging that it might also be true that the leaders were moving around.
The spokesman said it was a "very positive discussion" between the two premiers this morning.
"There is no division at all in what we are trying to achieve, which is bring to a conclusion the successful outcome of what we are trying to achieve in Afghanistan.
"We will not be able to achieve that if we don't work closely with Pakistan."
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