Australia may be forced to accept three Islamic State fighters in Turkish custody as Ankara begins repatriating foreign fighters to their homelands.

Turkey has so far sent up to 10 fighters back to Britain, the US and Germany, saying it cannot continue to house them, even as the governments have rejected taking their fighters back and have cancelled passports.

The Australians are among 959 foreign IS fighters and families in Turkish custody in northern Syria.

Turkey's ambassador to Australia Korhan Karakoc told The Weekend Australian Ankara wants Canberra to co-ordinate the return of the men.

The defeat of Islamic State has left hundreds of foreign fighters including Australians in Turkish custody. (AAP)

Efforts were under way to repatriate "a few" suspected Australian ISIS prisoners, whom Mr Karakoc was unable to identify. But he said Turkey wants the Australian government to co-ordinate their return.

"Turkey, at this stage, is not in a position to take a unilateral step because we have to co-ordinate, at the end of the day," he said.

"It really requires some formalities. The Australian side should be willing to accept them.

"We certainly want to send them away so you can handle them here in their country. But it would take some time."

He also said the Australian government was reluctant to take the men back.