The former head of the CIA's counter-terrorism centre has warned that the use of drone strikes in Yemen risks turning militants into "dedicated enemies of the west".

Robert Grenier, who was director of the intelligence agency's counter-terrorism unit from 2004 to 2006, said the US risked turning Yemen into the "Arabian equivalent of Waziristan", a reference to the strife-torn Pakistani region.

His comments came after the resignation of the US ambassador to Pakistan, Cameron Munter, who is said to have clashed with the CIA over its drone programme. On Sunday, a US drone attack in Yemen killed a top al-Qaida leader who was on the FBI's most wanted list.

"One wonders how many Yemenis may be moved in future to violent extremism in reaction to carelessly targeted missile strikes, and how many Yemeni militants with strictly local agendas will become dedicated enemies of the West in response to US military actions against them," Grenier wrote in a comment article for Al Jazeera.

"[Al-Qaida in the Arabian peninsula] and those whom it trains and motivates to strike against civilian targets must continue to be resisted by the joint efforts of the civilised world.

"But the US would be wise to calibrate its actions in Yemen in such a way as to avoid making that obscure and relatively limited and containable threat into the Arabian equivalent of Waziristan," he wrote.

Grenier's comments come after Munter resigned on Monday. The former ambassador to Islamabad had only been in the job for two years, but some reports have suggested he had clashed with Washington over his urging for fewer drone strikes.

The Pentagon announced in January that the US will increase the numbers of its unmanned drones by almost a third over the next decade, while reducing its military. The defence secretary, Leon Panetta, said the number of soldiers in the US army would be cut from around 570,000 to 490,000, while reports suggested 30% more drones would be developed as the military shifted its focus from conflict in Iraq and Afghanistan to potential challenges in Asia.

It was a drone strike, carried out by the CIA, that killed Fahd al-Quso in Yemen last weekend. Quso, who featured on the FBI's most-wanted list, was sought for his role in the 2000 bombing of the warship USS Cole. He was killed by a missile on Sunday as he stepped from his vehicle in the southern Shabwa province, Yemeni officials said.

It emerged on Thursday that the agent who had helped to foil an "underwear" bomb plot in Yemen had also played a central role in Quso's death. The agent, who was recruited by al-Qaida to carry a bomb onto a US-bound plane, handed the device over to US authorities instead. It has since been confirmed that the agent is a British citizen of Saudi origin, causing an awkward scenario for MI5 and MI6, whose agents are banned from missions that lead to assassinations.