Pakistan's foreign ministry said it had called Anne Patterson to register "a strong protest" over a number of missile attacks by US drones inside its territory.
"Our ambassador will certainly go in and see the Pakistanis anytime they want to see her about these issues," Perino said.
George Bush, the US president, believes that "Pakistan has a very serious problem" with extremism and that authorities there "recognise how serious that problem is," the spokeswoman said.
"We remain very concerned, but we remain willing to work with them," she said, underlining that Pakistan had "very serious issues when it comes to their economy as well".
Perino spurned any suggestion that the US's military activity was fuelling resentment against the US and stoking extremism rather than fighting it, denying "that we incited that, that it was our fault that terrorists attack".
"Terrorism is something that needs to be confronted," she said.
"The Pakistanis themselves, the innocent Pakistanis, they also deserve to be protected from terrorists and so we'll continue to work with them."
Sean McCormack, a US state department spokesman, acknowledged "bumps in the road and disagreements" in US-Pakistan co-operation on counter-terrorism efforts but also refused to comment on the latest dispute.
"The Pakistani government also understands that it is in their vital national interest to address the threat from violent extremists," he said.