The attacks have ratcheted up tensions between the nuclear-armed countries, which have fought three wars in the last 60 years.
Asked about the possibility that India may take military action if Pakistan does not react to its allegations, McCain said he believed Islamabad would cooperate with India and take timely "specific acts to avert any further deepening of this crisis.
"From our meetings we have had today we are encouraged that the government of Pakistan will show that cooperation in words and deed," he told reporters after meetings with Pakistan's prime minister and military chief.
McCain came to Pakistan with two other U.S. senators - Joseph Lieberman and Lindsey Graham - as part of a regional tour as members of the Senate Armed Services Committee. They previously visited India.
Lieberman said he was encouraged that Pakistan "will not allow the terrorists to divide this country from either its allies in Washington or its neighbors in New Delhi."
The attacks have triggered an intense round of diplomacy to stop relations between the two countries deteriorating, something Washington fears will affect its campaign against al-Qaida in the region.
Earlier, the government denied reports that a man pretending to be India's foreign minister spoke to President Asif Ali Zardari over the phone during the Mumbai attacks.
Dawn newspaper reported the alleged hoax call Saturday, and said it prompted Pakistan to put its air force on high alert. A security official later said a man pretending to be Foreign Minister Pranab Mukherjee had spoken to him in a "threatening manner."
But Information Minister Sherry Rehman said in a statement that the call "was placed from a verified official phone number of the Indian Ministry of External Affairs."
She did not explicitly say that the call was from Mukherjee, but two other government officials said it was him. They spoke on condition of anonymity because of the sensitivity of the situation.
Pakistan says it has yet to see any proof of New Delhi's allegations that its citizens were involved in the Mumbai attacks, but is prepared to cooperate with India. It has denied any of its state agencies were involved, noting it too is a victim of terrorism.
In the latest attack, a car bombing Friday in the northwestern city of Peshawar killed 29 people and wounded 100 more. The blast wrecked a Shiite Muslim mosque and a hotel, but the motive and culprits were not immediately known.
