Panetta, who arrived in Islamabad yesterday, presented the evidence during meetings with Pakistan army chief Gen Ashfaq Parvez Kayani and Inter-Services Intelligence (ISI) head Lt Gen Ahmed Shuja Pasha late last night, media reports said today.
The CIA had passed intelligence in the past few weeks to its Pakistani counterparts on two facilities where militants made Improvised Explosive Devices (IED) but when Pakistani forces raided the facilities, the militants had disappeared, the reports said.
Panetta showed Pasha "satellite and other intelligence that the CIA believes is evidence of Pakistani security's efforts to help Islamic militants based in Pakistan," ABC News quoted US and Pakistani officials as saying.
The CIA chief shared with the Pakistani Generals a "10-minute edited video that shows the militants evacuating two bomb factories in Waziristan," Time magazine quoted its sources as saying in a report on its website.
One of the bomb factories is based at Miranshah in North Waziristan and the other is in South Waziristan.
The militants in North Waziristan are believed to belong to groups led by Hafiz Gul Bahadur and Sirajuddin Haqqani, whose men target US and NATO troops across the border in Afghanistan.
Both Bahadur and Haqqani are also believed to have peace deals with the Pakistan army.
During his meetings, Panetta conveyed the CIA's belief that the militants had been warned by Pakistani security officials prior to the raids, ABC News reported.
Panetta travelled to Islamabad just hours after his Congressional hearing to become Secretary of Defence, a trip that US officials described as a way to "discuss ways to improve cooperation".
However, his visit expected to be his last as CIA chief "underscored the lack of trust that US officials continue to have in their Pakistani counterparts," ABC News said.
Since the killing of Osama bin Laden in a US raid in Abbottabad on May 2, the US has urged Pakistan to take "decisive steps" to crack down on militants and handed over a list of five top terrorists, including Ayman al-Zawahiri and Ilyas Kashmiri, that it wants Islamabad to apprehend or kill.
US and Pakistani officials admitted that the escape of militants from the bomb-making facilities was a "setback," ABC News reported.
Pakistani officials made a "rare admission that some kind of collusion was possible."
"There is a suspicion that perhaps there was a tip-off...It's being looked into by our people, and certainly anybody involved will be taken to task," a senior unnamed Pakistani official told the Washington Post.
Referring to efforts to revive intelligence cooperation between Pakistan and the US, another American official told The Washington Post: "We are willing to share, but you have to prove you will act. Some of your people are no longer fully under your control."
Overhead surveillance video and other information on the bomb making facilities was given to Pakistani officials in mid-May, the Post reported.
One was located in a girls' school in Miranshah, home to the Haqqani network's North Waziristan headquarters.
The other, in South Waziristan, was believed to be an Al Qaeda-run facility.
When Pakistani military units arrived at the sites on June 4, they found them abandoned, the Post reported.
Meanwhile, a US Congressional report has said that since 1948 Pakistan received over USD 30 billion aid from America, two third of which came after 9/11 attacks.
"Some question the gains from the aid, saying there is a lack of accountability and reform by the Pakistani government, and any goodwill generated by it is offset by widespread anti-American sentiment among the Pakistani people," Congressional Research Service (CRS) informed members of the Congress in a 47-page internal report.
"Recent major developments, including the killing of Al Qaeda founder Osama bin Laden in Pakistan, have put strains on bilateral relations, making uncertain the future direction of US aid to Pakistan," it said.
For many lawmakers, the issue will be how to balance considerations about Pakistan's strategic importance to the United States with the pervasive and mounting distrust in the US-Pak relationship and with budget deficit-reduction pressures, the report said.