Pakistan should stop protesting against US missile strikes in its territory and instead focus on extracting concessions for what it sees as a violation of sovereignty, analysts said.

The first suspected US missile strikes since US President Barack Obama took office destroyed two alleged militant dens on Friday in the northwest tribal belt. Officials put the death toll at 21, including three children.

Sparking heavy criticism from the Pakistani government, the strikes dashed hopes that the new administration in Washington would halt such attacks in the fight against extremists in South Asia.

Political analysts stress that expectations of a policy change are unrealistic despite Washington's appointment of a new special envoy for Afghanistan and Pakistan and the Obama administration's pledge to reinvigorate diplomatic strategy.

Former interior minister and retired lieutenant general Hamid Nawaz said Pakistan had to work harder in the national interest to extract concessions elsewhere and overcome the clear violation of national sovereignty.

"They (the US) are very serious as far as terrorism is concerned. The new US administration is deploying additional troops in Afghanistan and when General David Petraeus was here, he was concerned about the supply route (to the troops)," he said.

The United States is seeking to increase the number of supply routes into Afghanistan, where US and NATO forces are fighting Taliban insurgents, with extremist attacks plaguing the main transport corridor through Pakistan.

"The US may help Pakistan more in terms of giving more aid, offering more trade opportunities, relaxing pressure on the nuclear programme or helping us improve relations with India," Nawaz said.

"Pakistan has to take decisions in the national interest. There is no use in protesting to the United States. We will have to take action," said Nawaz.

"We can tell them 'do not violate our sovereignty and if you do we will stop the supply route', things like that, so that our voice is heard in Washington."

Ishtiaq Ahmed, an international relations professor at Islamabad's Quaid-i-Azam University, also hinted at some kind of quiet agreement.

"There might be an understanding at some levels between the two sides about the US drone attacks in Pakistani tribal areas," he told AFP.

"Protests by Pakistan over missile strikes are basically meant for domestic public consumption, otherwise it is not possible that we keep on protesting and they keep on doing it," Ahmed said.

Former president Pervez Musharraf also said recently that Pakistan's efforts in the fight against terror should be rewarded with greater assistance.

On the eve of Friday's strikes, Obama warned that Islamist extremists in Pakistan and Afghanistan posed a grave threat and would be tackled as a single problem under a wider strategy.

Dozens of missile strikes since August have sparked government criticism of the United States, a close ally fighting the Taliban in Afghanistan and believed to be firing the missiles from unmanned CIA aircraft.

"These attacks do not help the war on terror, it alienates the local population," said a spokesman for President Asif Ali Zardari after the head of state lunched with US ambassador Anne Patterson on Saturday.

"We maintain that these attacks are counter-productive and should be discontinued," said the foreign ministry spokesman.

Islamabad has welcomed Obama's appointment of veteran US diplomat Richard Holbrooke as special Afghanistan and Pakistan envoy, who has been nominated for the Nobel Peace Prize seven times and is best known for brokering the 1995 peace agreement that ended war in Bosnia.

Political analyst Hasan Askari said that while Washington pursues a double-pronged strategy, a full-scale review was underway.

"The US administration appears to be very active on Afghanistan... there are drone attacks and on the political front they have appointed a special envoy for Pakistan and Afghanistan. They are reviewing policy," Askari told AFP.