The coup attempt in Turkey has yielded its first tangible disruption to the war against Islamic State, as the Pentagon has temporarily lost access to the Turkish airfield it uses as its primary staging ground for its air campaign in Syria and Iraq.

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Although the Pentagon press secretary, Peter Cook, on Saturday portrayed the interruption as surmountable, there was no indication as to when the US would regain access to the Incirlik airbase in south-eastern Turkey, as a defiant Turkish elected government has begun arresting thousands of military officers and soldiers in reprisal for the failed coup.

Turkish airspace, including that over the Incirlik airbase, was closed to military aircraft – some of which flew above Ankara during the attempted takeover on Friday night.

“US officials are working with the Turks to resume air operations there as soon as possible,” Cook said in a statement, reversing an assurance on Friday that the then unfolding coup would not immediately affect the Isis campaign.

“In the meantime, US air forces central command is adjusting flight operations in the counter-Isil campaign to minimize any effects on the campaign,” said Cook, adding that the US-operated facilities at the airbase were unaffected by a broader outage to commercial power in the country.

In addition to Iraqi military airfields open to US warplanes, the aircraft carrier USS Dwight D Eisenhower is in the Persian Gulf. But while last month the US briefly had two carriers in the eastern Mediterranean – the Eisenhower, en route to the Middle East, and USS Harry S Truman, which returned to its Norfolk, Virginia, home port on 13 July – it currently has none in the waters nearest to Syria.

Christopher Harmer, a former navy officer turned analyst for the Institute for the Study of War, said loss of access to Incirlik would place a “significant” strain on the air war if it lasted beyond four days, as the strain of constant flight-deck operations would then eat into scheduled rests for maintenance and fuelling.

“A 48- to 72-hour disruption shouldn’t have a big impact, but if it’s longer than 96 hours, it’s going to have a big impact and the longer it lasts, the bigger the impact,” Harmer said.

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Furthermore, the longer the Incirlik closure lasts, the fewer drone strikes the US is likely to launch in Syria, since the US does not field in its drone fleet a robotic aircraft capable of launching from and landing on an aircraft carrier deck.

The Turkish base is also home to A-10s, the most reliable manned aircraft the US possesses for providing air support to ground forces fighting Isis.

The US air force in the Middle East indicated it was prepared to keep up its operational tempo against Isis, also called Daesh and Isil, without Incirlik.

“The air war operates out of multiple locations,” said Lt Col Chris Karns, a spokesman for US air forces central command. “While Incirlik is certainly important, it is one of several locations where air operations are executed. We are making adjustments to ensure impacts to operations are minimized.

“The situation will likely be fluid but flexibility has always been foundational to the way this war has been and will be fought. Getting after Daesh will continue to occur.”

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Cook also said the US was in the process of ensuring the safety of thousands of US military personnel, their families and other civilians in Turkey.

“All indications at this time are that everyone is safe and secure,” he said.

The Turkish prime minister, Recep Tayyip Erdoğan, is considered in Washington an erratic and unreliable ally against Isis, only allowing its Nato partner access to Incirlik to fight the group in 2015.

As Erdoğan and his government have blamed Fethullah Gülen, a cleric currently exiled in Pennsylvania, for the coup, and are urging the US to hand him over, Harmer said it was possible that Erdoğan had closed Incirlik as a gambit to force the Obama administration to extradite him.

In light of the coup attempt, Erdoğan “can close access to air bases to the US that he couldn’t a week ago”, Harmer said.