In an interview with the BBC radio, Musharraf was asked for his response to the view that Pakistan was not a good ally in the fight against global extremism because of links between terrorism and his country.
"You will be brought down to your knees if Pakistan doesn't cooperate with you. That is all that I would like to say. Pakistan is the main ally. If we were not with you, you would not manage anything. Let that be clear," he said.
"And if the ISI (Inter Services Intelligence) is not with you, you will fail. Let that be very clear also. Remember my words: if the ISI is not with you and Pakistan is not with you will lose in Afghanistan."
Musharraf recorded the interview after talks with British Prime Minister Tony Blair in London on Thursday. The meeting came following a leaked British defence ministry think-tank report that claimed the ISI was indirectly supporting extremism in Afghanistan, Iraq and Britain by backing the Muttahida Majlis-i-Amal.
President Musharraf again strongly denied the claims, which were written by a senior military official linked to Britain's foreign intelligence service, MI6, after a fact-finding mission there in June. The President accepted Blair's assurances that the document was not a reflection of the British government position.
In the BBC interview, Musharraf pointed to ISI and Pakistan army successes in the US-led "war on terror", in particular the capture of hundreds of suspected al Qaeda militants. They included the alleged mastermind of the September 11, 2001 attacks Khalid Sheikh Mohammed, he said, while they played a key role in foiling an alleged terror plot to blow up US-bound passenger jets on August 10 this year.
The President called for more understanding of his country's predicament as it struggled with the continuing fallout from the Cold War played out by proxy in Soviet-occupied Afghanistan in the 1980s.
"From 1979 to 1989 we fought the Soviet Union for you. We won the Cold War for you," he said, explaining that the Pakistan army and ISI played a part in training the tens of thousands of Mujahideen fighters to resist the Soviets.
But after the Soviet withdrawal, the West left Pakistan "high and dry", he said, leading to the creation of the radicalised Taliban and al Qaeda from the remnants of the Mujahideen resistance.
"The world must understand our problem. It is for you that we did it and we are suffering," Musharraf told the broadcaster. "Our national fabric has been torn. "Now, without understanding, everyone blames us for what is happening in Pakistan. It is something that is happening, understand it and help us."