Panetta was scheduled to meet Pakistan Army chief Gen Ashfaq Parvez Kayani, sources said.
He will also meet Inter-Services Intelligence chief Lt Gen Ahmed Shuja Pasha and top civilian leaders.
US Secretary of State Hillary Clinton and Pakistan Prime Minister Yousuf Raza Gilani yesterday said that the two countries would work together to ensure that Al Qaida is "dismantled, disrupted and defeated".
Gilani said it was "imperative to make a distinction between the Taliban and Al Qaida, which would help to overcome the threat".
Gilani and Clinton also expressed satisfaction over the establishment of a Joint Task Force between the intelligence agencies of the two countries to facilitate information-sharing and coordination.
Clinton had said the CIA chief would visit Pakistan for talks on cooperation.