Ahead of Gates' trip, one Nato official said: "We can't be successful unless Pakistan is part of the equation in eliminating this insurgency."
While Islamabad agrees that the refugee camps on its side of the border have become recruiting grounds for the Taliban, Pakistani officials reject blame for the rising violence in Afghanistan.
Musharraf has refused to take sole responsibility for the border and said the Taliban is Afghanistan's problem.
The Pakistani foreign minister on Saturday called for more help and less rhetoric from the US to stop the flow of fighters.
Khursheed Mehmood Kasuri told Reuters at a security conference in Munich on Saturday: "Simply making a rhetorical appeal - stop extremism - if it were that simple it would have been resolved long ago in Palestine, in Lebanon and Iraq and in Afghanistan. Obviously it's more complicated."
Gates travelled to Pakistan after four days of meetings in Spain and Germany which focused on the war in Afghanistan. Last year was Afghanistan's bloodiest since the US-led invasion in 2001 and the Taliban has promised a spring offensive of thousands of suicide bombers.
While Nato commanders and US officials increase pressure on Pakistan, many also say the Pakistani government has taken some steps to address the problem.
A senior US defence official travelling with Gates said: "It's just a fact that there's a sanctuary in Pakistan.
"I think we give the government of Pakistan credit for asserting itself in many significant ways, many unprecedented ways, but clearly there's still a problem."