A Pakistani journalist whose relatives were killed in a US drone strike has started a legal push to charge America's top spy in Pakistan with murder.

"We appeal to the authorities not to let Jonathan Banks escape from Pakistan," said Karim Khan, naming the alleged CIA station chief in Islamabad. "He should be arrested and executed in this country."

Khan was speaking outside an Islamabad police station after lodging an application to prevent the US official from leaving Pakistan. He has lodged a separate civil suit seeking $500m (£314m) in damages from the US government.

Khan says that his brother and son, both government employees, were killed in a CIA drone strike on their home near Mir Ali in North Waziristan in December 2009.

Press reports named the target as Haji Omar, a leading Taliban commander. Khan insists that Omar was not in the house and that his relatives were innocent. "These men had nothing to do with the Taliban," said his lawyer, Shahzad Akbar.

Mir Ali is a hotbed of al-Qaida and Taliban militancy that has borne the brunt of a sharp escalation in US attacks this year. Akbar said his client has identified Banks as the CIA station chief through local press reports; one local paper recently claimed that Banks had entered Pakistan on a business visa and therefore does not enjoy diplomatic immunity.

Khan's allegations are difficult to confirm independently. Information about civilian deaths from US drone strikes is widely disputed, largely because the lawless tribal belt is out of reach to foreign and even most Pakistani journalists. His unusual legal bid has slim chances of success. The CIA has rarely been successfully sued at home, much less abroad. And the recent WikiLeaks cables revealed secret Pakistani government support for the drones.

As Khan lodged his legal papers today, the CIA deputy director, Michael Morell, met prime minister Yousaf Raza Gilani on the other side of Islamabad. But the case could revive public debate about the drones, whose legality was also questioned in a report by a UN human rights investigator last June. Pakistani public opinion is mostly hostile to drones, although criticism has abated somewhat this year. "I don't think we will achieve anything immediately, but we have started something," said Akbar. "Before this, nobody was thinking of the legality of the drones."

The drones are already a subject of lively debate inside the American system, the WikiLeaks cables showed. Last year ambassador Anne Patterson argued that increased "unilateral operations" risked "destabilizing the Pakistani state" and ultimately hindering the US goal of expelling al-Qaida from the region.