Pakistani authorities on Thursday launched a formal investigation into the CIA's former station chief in Islamabad. He's accused of murder and conspiracy in connection with the agency's lethal drone program, which resulted in the deaths of civilians in a covert operation in Pakistan five years ago.

Jonathan Bank is a veteran CIA officer, and also a controversial one. Last year, he was placed on paid administrative leave and removed from his position as the agency's chief of Iran operations after an internal CIA review concluded he had created a hostile and abusive work environment, according to the _Los Angeles Times. _Three former officials who spoke with the newspaper said the Iran operations division "was in open rebellion to Bank's management style, with several key employees demanding transfers." He was subsequently barred from a management position for a year.

The investigation targeting Bank was announced exactly one week after the White House revealed in an extraordinary public statement that two botched drone strikes conducted by the CIA killed two hostages, one of whom was an American, and two American members of al Qaeda in Pakistan last January.

The so-called "signature strikes," which allow the CIA to strike a person not based on who he is but rather his "suspicious" pattern of behavior, have deepened the debate about the Obama administration's controversial use of the drones, and about the accuracy of intel used to establish targets. The CIA inspector general has launched a review into the January operations.

The criminal investigation into the December 2009 drone strike is the first time another country has taken steps to hold individual CIA officers accountable for their alleged roles in the CIA's drone program, according to the international legal organization Reprieve, which represents Kareem Khan, whose son and brother were killed in the strike.

Earlier this month, the Islamabad High Court ordered the police to launch a criminal investigation into Bank and former CIA general counsel John Rizzo. It was unclear at the time whether the police were going to appeal the decision. On Thursday, however, Islamabad police decided to press forward and comply with the court order.

However, police said they intend to transfer the case to the secretariat of the Federally Administered Tribal Area, which has jurisdiction in Mir Ali in North Waziristan, where the strike occurred. Distrustful of the move, Reprieve lawyers said they would file a motion with the Islamabad high court next week seeking to block it.

The CIA declined to comment to VICE News. (Neither the agency nor the Obama administration has formally acknowledged that the drone strike took place.) News reports published at the time said three people were killed. Pakistani intelligence officials asserted that the men were insurgents, but failed to offer evidence to back up the claim.

A handwritten criminal registration document filed by Khan with Islamabad police in 2010 [pdf below] says that the drone strike took place on New Year's Eve 2009 in a tribal area, and that his house was "attacked with missiles fired by unmanned aerial vehicles (UAV) also known as drone, which is believed to be operated by Central Intelligence Agency."

"At the time of the missile attack three people were present… who died due to this attack," Khan wrote. "One was undersigned's brother [and 35-year-old English teacher] Asif Iqbal. The second person was undersigned's [teenage] son named Zahin Ullah Khan. The third person who lost his life to this drone attack was a mason named Khaliq," who was a construction worker residing in Khan's house. The home was reduced to "rubble" as a result of the strike.

Bank is referred to as "Banks" in the criminal registration. He was removed as Islamabad station chief in 2010 after a handful of international newspapers published his name in connection with the charges against him leveled by Khan, who threatened to sue the CIA for $500 million. Protesters who took to the streets following the attack carried signs with emblazoned with Bank's name. CIA officials have privately claimed that Bank's identity was leaked by Pakistan's intelligence agency, Inter-Service Intelligence (ISI), in retaliation for the CIA's drone strikes in the region.

Khan alleges in his complaint that Bank "and his clandestine network… ordered/conspired to target" his house in "clear violation of Pakistani law" and Pakistan's sovereignty.

"The names of the remote pilot of said drone and others involved is not know at the moment but can be ascertained through interrogation of Jonathan Banks," he wrote.

Mirza Shahzad Akbar, a legal fellow with Reprieve who is based in Pakistan, is Khan's lawyer. He said the decision by Islamabad police to formally investigate Bank and the CIA marks a "key turning point in Kareem Khan's search for justice over the deaths of his brother and son."

"After four years of government attempts to block his case, Kareem may finally get the answers he deserves and the CIA may finally be held in some way accountable for the murders it has been carrying out on Pakistani soil," He said.

He also claims that the orders to strike Khan's family came from the US embassy in Islamabad, where Bank and other CIA officers were based, and that's why jurisdiction over the investigation should remain with Islamabad police.

According to statistics compiled by the UK-based Bureau for Investigative journalism (TBIJ), between 2,449 and 3,949 people have been killed in 415 drones strikes in Pakistan between 2004 and 2015. Of those killed, between 423 and 962 were civilians.

Last week, Senator Dianne Feinstein, the former chairwoman of the Senate Intelligence Committee, which conducts oversight of the CIA's drone program, claimed that TBIJ's figures are wildly exaggerated.

"The collateral damage has been extraordinarily low, and that's really fact," Feinstein told reporters. "And I only wish I could tell you what it was. And that's the irony here, that this is all classified and it's very difficult to speak about it in any kind of full way."

The information remains classified because Feinstein and her Republican counterpart on the committee, Saxby Chambliss, agreed to honor a request from Director of National Intelligence James Clapper to pull a provision from an intelligence spending bill, drafted by Feinstein, that would have called upon President Barack Obama to reveal in an annual report the number of "combatants" and "non-combatants" killed in drone strikes. The provision was removed because it would have held up passage of the bill.

Feinstein renewed her call for an annual accounting on the number of civilians and combatants killed in drones strikes after the White House released details about the January drone strike that resulted in the accidental deaths of two hostages and the two American Al Qaeda militants.

Meanwhile, according to the Associated Press, Bank is now back at the CIA, and has been named deputy chief for counterintelligence at the Counter Terrorism Center, the division that oversees and conducts drone strikes.

Follow Jason Leopold on Twitter: @JasonLeopold