Defence secretary Leon Panetta has upped US criticism of Pakistan's jailing of a doctor who helped track down Osama bin Laden, suggesting it had hit efforts to steer diplomatic relations between Washington and Pakistan back on track.

Speaking on ABC's This Week, Panetta said the 33-year prison sentence handed to Shakil Afridi for treason was "so difficult to understand and so disturbing".

The physician ran a fake vaccination programme to collect the al-Qaida chief's DNA as part of a CIA scheme to prove he was living in the Abbottabad compound where he was eventually killed.

Last week, the US Senate committee retaliated for the sentencing by voting to cut Pakistan's aid by $1m for each of the 33 years handed down to Afridi.

The spat has served to worsen already rocky relations between Washington and Islamabad amid tension over Pakistan's closure of a supply route to Afghanistan and the US's use of unmanned drones to strike at terrorist targets.

Panetta described the diplomatic conditions between the two countries as "up and down", noting "this is one of the most complicated relationships we have had".

But he stressed the importance of trying to improve links between Washington and Islamabad.

Nonetheless, his criticism over the handling of Alfridi was firm.

"This doctor was not working against Pakistan. He was working against al-Qaida, and I hope Pakistan understands that because what they have done here doesn't help re-establish a relationship between the United States and Pakistan."

The apparent leaking of information about the fake vaccination scheme by Pakistani authorities – which was first reported in the Guardian – has angered the US at a time of heightened tension between the two countries.

However, after Afridi's role was made public, American officials openly acknowledged it.

Panetta – who was CIA director when Bin Laden was killed– described the doctor as having been "very helpful" in gathering intelligence on the al-Qaida leader.

The defence secretary also told This Week that the continued use of part's of Pakistan's border region as a safe haven for terrorists remains a concern that needs to be addressed.

But he defended the Nato plan to end active military operations in Afghanistan by the end of 2014.

"That is the plan that has been agreed and it is a plan that it working," he said. However, he committed the US to an "enduring presence" in the strife-torn country beyond that date.