General Musharraf said that most fighters originated in Afghanistan and were led from there.
"A misperception is being created that the resurgence of Taliban is from Pakistan. This is absolutely wrong. The resurgence of the Taliban is in Afghanistan, but some support goes from Pakistan," he said.
He announced the army he leads would soon fence parts of the porous border to stop fighters' infiltration, despite Afghan opposition.
Musharraf's robust defence of Pakistan's efforts in the US-led "war on terrorism" - and frank admission of lapses - follow criticism from US military officials who say cross-border attacks into Afghanistan have risen threefold since Pakistan signed a September peace deal with pro-Taliban fighters in its North Waziristan region.
Musharraf said there had been "some incidents" of security forces at isolated border posts "turning a blind eye".
He cited an example of two guards, located 500 metres from their section base, being outnumbered by around 20 highly trained and motivated al-Qaeda fighters.
"I would imagine that others may be doing the same thing," he said.
Extra security Pakistan would give extra security to such border troops so they "feel strong enough and secure enough to check (people at the border) and that they won't be killed", he said.
But he denied any official collusion with the fighters - including by the powerful Inter-Services Intelligence - which he said was staffed by army officers who obey the chain of command.
"There is no question of anyone abetting," Musharraf said. He announced Pakistan had begun preparations to fence seven or eight locations - a total of 35km - along its northwest border, which he said would take a "a few months" to complete.
They would not use land mines because of concerns raised by the international community, Musharraf said.
However, he said plans for a second phase still foresaw using both fencing and mines to secure 250km of the border further south, in Baluchistan province.
"No one has the right to criticise unless they come up with an alternative solution ... if there is no (other) solution, we will do it our way," Musharraf said.