The 33-year prison term imposed on Shakil Afridi following a treason conviction will do nothing to improve "one of the most complicated relationships that we've had," Leon Panetta told ABC's "This Week."
"It is so difficult to understand and it's so disturbing that they would sentence this doctor to 33 years for helping in the search for the most notorious terrorist in our times," Panetta said.
"This doctor was not working against Pakistan. He was working against al-Qaida. And I hope that ultimately Pakistan understands that, because what they have done here ... does not help in the effort to try to re-establish a relationship between the United States and Pakistan."
Afridi ran a fake vaccination program aimed at collecting DNA from the bin Laden family in the town of Abbottabad, where the al-Qaida leader died in a U.S. Navy SEALs raid on his hideout a year ago.
Pakistani lawyers said Friday they would appeal the conviction handed down by a tribal court, a primitive system of justice that's the law of the land in the country's semi-autonomous tribal belt.
The doctor, meantime, is about to be transferred into a high-security prison outside of Peshawar due to fears he could be set free in some sort of clandestine operation, Pakistan's The Nation reported on Sunday.
Prison officials are to meet with government authorities on Monday to discuss where Afridi could be safely held. The doctor also faces a threat within the Peshawar jail from Taliban also imprisoned there who have vowed to avenge the death of bin Laden.
Afridi's sentence has so angered American lawmakers that a U.S. Senate panel voted last week to slash aid to Islamabad by $33 million — $1 million for every year of Afridi's sentence.
Yet Pakistan remains an important nation in the region because it possesses nuclear weapons, Panetta said.
"Our responsibility here is to keep pushing them to understand how important it is for them to work with us to try to deal with the common threats we both face," Panetta said.
"And what they did with this doctor doesn't help in the effort to try to do that."
A White House attempt to reach out to Pakistan by issuing a last-minute invitation to the NATO conference in Chicago last week didn't have the intended outcome.
The Obama administration had hoped that if Pakistani President Asif Ali Zardari shared the spotlight with other global leaders, it might help convince him to reopen the country's supply routes so that vital supplies can reach NATO troops fighting in Afghanistan.
He refused, reportedly irritating President Barack Obama to such an extent that he pointedly failed to mention Pakistan while publicly thanking Russia and central Asian nations "that continue to provide critical transit" of war supplies into Afghanistan.
Zardari sat just a few feet away during Obama's remarks.
Retired Pakistani military officials said Saturday that Pakistan was treated as an "accused" at the summit.
The executive council of the Pakistan Ex-servicemen Association said government officials should have counselled Zardari to skip the conference since neither Obama nor other NATO leaders would commit to formal meetings with him.
The Pakistani leader and Obama spoke briefly on the sidelines of the conference.
The association said that Pakistan has served U.S. interests for over six decades, but "our sacrifices and contributions" have been totally forgotten.
In talks on reopening the supply routes with Secretary of State Hillary Clinton, Zardari has made several demands, including a review of the U.S. policy of drone attacks against targets inside Pakistan and a public apology for the killing of its troops.
He also wants higher charges for each vehicle using Pakistan's supply routes, from US$250 per vehicle to as much as $5,000.
"NATO containers have been taking free rides for the past 11 years causing damage worth billions to infrastructure," said the Pakistan Ex-servicemen Association's communique.
"Now our demand to charge them is termed as extortion, which proves that bilateral relations have reached their lowest ebb."