Sources privy to the meeting said differences cropped-up between the two intelligence chief's after General Pasha criticised the United States for its failure to help Pakistan in its counter-terror efforts.
Sources said, during the meeting, expressed his disappointment over CIA's failure to provide credible information to Islamabad regarding the extremist groups working in Afghanistan to create trouble in Pakistan.
Panetta is visiting Pakistan as a follow-up to the US of Secretary of State Hillary Clinton's visit to address complains of the Pakistan's army, The Nation reports.
He also held separate meetings with Pakistan President Asif Ali Zardari, Prime Minister Yousuf Raza Gilani and Chief of Army Staff General Ashfaq Kayani.
Insiders said the CIA chief discussed at length issues regarding military-to-military cooperation and intelligence sharing to make joint efforts against terrorism more effective during his meeting with Pasha.