The foreign ministry of Pakistan has condemned the strikes as a violation of the country's sovereignty

US drones have fired missiles at militant hideouts in north-western Pakistan, killing 13 suspected insurgents and marking the resumption of the CIA-led programme after a nearly six-month break, officials said on Thursday.

The Pakistani foreign ministry condemned the strikes as a violation of sovereignty. The attacks came days after a five-hour siege of Karachi airport left 36 people, including 10 militants, dead which raised concerns over Pakistan's ability to deal with the Pakistani Taliban, who said they had carried out the assault along with an Uzbek militant group. It was not immediately clear if the drone strikes were connected to the airport attack. Pakistan had asked the US to halt drone strikes while it was trying to negotiate a peace deal with the militants, but even before the airport siege those talks had largely collapsed.

The focus has shifted to whether Pakistan's prime minister, Nawaz Sharif, will authorise a large-scale military offensive against the North Waziristan tribal areas where the militants are headquartered. In the first strike, late on Wednesday, a suspected US drone fired two missiles at a militant hideout in North Waziristan near the Afghan border, killing three people.

Then, early on Thursday, another suspected US missile strike targeted a separate militant compound in North Waziristan, killing at least 10 people, Pakistani intelligence officials said.

Pakistan's north-west, particularly North Waziristan, is home to numerous militant groups – both local and al-Qaida-linked foreign groups – which often work together, sharing fighters, money or expertise.

There was no immediate information on the identities of those killed in the operation but the two intelligence officials who gave information about the strikes said both were in areas dominated by the Haqqani network, and most of those killed are believed to have belonged to the organisation.

"We have also been hearing some names coming from our field agents, but we don't have any confirmation so far," said one of the officials. The officials spoke on condition of anonymity because they were not authorised to speak to the media.

The Haqqani network is believed to carry out operations against US and Nato forces in Afghanistan from bases in North Waziristan and is considered one of the more lethal groups operating in Afghanistan. It is believed to have been the organisation holding Bowe Bergdahl, a US prisoner of war recently released in exchange for five Taliban prisoners.

Due to stricter rules on the use of drones, diplomatic sensitivities and the changing nature of the al-Qaida threat, the number of US drone strikes had dwindled. The strikes on Wednesday and Thursday were the first since Christmas, and even before that the number of attacks every year had been steadily dropping.

The Pakistani government and military are believed to have supported the drone strikes to a degree in the past but in recent years have become more vocal in their opposition.

Meanwhile, a Pakistani court on Thursday struck down a government order barring the former military ruler Pervez Musharraf, who faces treason charges, from leaving the country. The government can still appeal.

The ruling by the Karachi court could pave the way for the man who ruled Pakistan for nearly a decade to leave the country after an embarrassing trial that saw him become the first chief of army staff to face treason charges.

It also puts the Pakistani government, whose decision to push for Musharraf's trial put it at odds with the powerful military, in a tricky position where it must decide whether it wants to further anger the military by trying to keep Musharraf from leaving the country.

Under the Karachi court ruling, the government has 15 days to appeal against the decision, so Musharraf can't leave Pakistan immediately.

The court gave no reason for striking Musharraf's name from the exit control list, which prevents people from leaving the country, usually in legal cases.

Musharraf, 70, took power in a 1999 coup and then stepped down in 2008. He later left the country, but returned in March 2013, hoping for a political comeback.

Instead, he got embroiled in court cases, including the treason charges, which are connected to his decision in 2007 to declare a state of emergency and detain senior judges, including the chief justice.