The Pentagon and the White House are pushing back on reports that the Obama administration is pausing drone strikes and other counterterrorism operations in Yemen, amidst the abrupt collapse of a critical partner government.

Rear Admiral John Kirby, the Pentagon’s chief spokesman, said both “unilateral and partnered” operations conducted by the US in Yemen against al-Qaida in the Arabian Peninsula (AQAP) “are not suspended”.

Continuing “partnered” strikes with the Yemenis provides a signal that the US still considers itself to have reliable allies on the ground to spot for drone strikes and aid in other attacks on an al-Qaida affiliate observers fear will capitalize on the unfolding unrest in the country.

Alistair Baskey, a spokesman for the National Security Council, said reports that counterterrorism in Yemen was on hold were “completely false”.

“As we have in the past, we will continue to take action to disrupt continuing, imminent threats to the United States and our citizens. We also continue to partner with Yemeni security forces in this effort,” Baskey said.

But as Houthi rebels marching on the capital of Sanaa have upended Yemeni politics and created uncertainty about continued cooperation with the US, Kirby said the military had “temporarily put on hold some training with the Yemenis”.

US Central Command, which oversees training for partner Middle Eastern military forces, declined to provide additional detail.

The resignation this week of President Abd Rabbo Mansour Hadi, whom the Obama administration had cultivated to permit drone strikes, has left many in US security circles wondering if a post-Hadi government will prove as acquiescent.

Under Hadi and his predecessor, the similarly deposed long-time dictator Ali Abdullah Saleh, the Yemeni government provided a launchpad for US attacks against al-Qaida’s local affiliate in return for hundreds of millions of dollars in economic aid, military equipment and training, and unequivocal diplomatic support.

A tally kept by the New America Foundation cited 19 drone strikes in 2014, down from a peak of 47 in 2012. US counterterrorism officials consider AQAP to be the terrorist network’s most potent affiliate, though its attempts to attack the mainland US have yet to succeed.

Both the Joint Special Operations Command and the CIA conduct separate drone operations in Yemen. The elite US forces have also sponsored their Yemeni counterparts, a relationship meant both to ease the counterterrorism burden on the US and to provide a durable tie to “deep state” security services in the event of political instability of the sort on display this past week.

Another insurance policy for US counterterrorism in Yemen is an airbase in Saudi Arabia, Yemen’s northern neighbor, which the CIA uses to launch drone strikes. The CIA declined comment about the impact of the Yemeni government collapse on its missions.

Anonymous US officials cited by the Washington Post said late on Friday that the US had lost its ability to work with Yemeni security services now under Houthi control, prompting what one called a “breather” in US strikes that would benefit al-Qaida.

It is unclear if military equipment provided by the US, from helicopters to communications gear, has fallen into anti-American hands, as happened earlier this year when Islamic State (Isis) militants overran Iraqi military positions. Several US military officials have declined to address whether the US even has knowledge of the fate of the weapons and other material it has for years provided to Yemen.

Reports from Yemen on Saturday indicated that local instability is continuing. Thousands reportedly took to the streets in Sanaa, demonstrating against the Houthi “coup” and chanting slogans denouncing al-Qaida. The Houthis are enemies of al-Qaida but not necessarily hospitable to the US.

An official quoted by the Washington Post said the US would be open to a counterterrorism dialogue with the Houthi leadership.