US-backed forces announced on Sunday the "final phase" of the battle to retake Raqqa in Syria, after the city was evacuated except for foreign Islamic State (IS) group militants and their families.

More than 3,000 civilians fled Raqqa on Saturday night under an evacuation deal that left just a few hundred foreign IS militants and some of their relatives in the handful of positions they still hold in their one-time Syrian stronghold.

Commanders said the way was now clear for a final assault by the Syrian Democratic Forces (SDF), a Kurdish-Arab militia alliance that broke into Raqqa in June and has since captured 90 percent of the city.

SDF spokesman Talal Sello said the 3,000 civilians had evacuated to areas controlled by the SDF under a deal negotiated between local officials from the Raqqa Civil Council and Syrian IS militants.

"Raqqa is now empty of civilians who had been taken as human shields," he said.

"Only 250 to 300 foreign terrorists who refused the deal and decided to stay and fight until the end remain in the city, and relatives of some members are with them," he said, without specifying the number of civilians.

Sello said a total of 275 Syrian IS militants and family members had also left militant-held parts of the city and were with SDF fighters.

He declined to specify where those militants and their families would go.

With the deal's implementation, the SDF announced what it said was the last phase of the fight to capture the city.

"We are now in the final phase of the battle for Raqqa," Jihan Sheikh Ahmed, spokeswoman for the SDF's Raqqa campaign, told AFP.

In a statement, the SDF said that the last phase of the fighting would "end the presence of the terrorist mercenaries inside the city".

"The battle... will continue until the entire city is cleared of terrorists who refuse to surrender, including foreign terrorists."

'Surrender or fight'

There had been speculation for days about a deal to allow the SDF to capture the last parts of the city while preventing further civilian casualties.

But there had been contradictory reports about whether the deal would allow foreign IS militants to leave, something that has been strongly opposed by the US-led coalition supporting the SDF.

The Raqqa Civil Council issued a statement Sunday afternoon denying that foreign IS militants had been allowed to leave the city, after one of its members said "a portion of the foreigners have left".

The RCC said "for clarification and accuracy, the foreign Daesh (IS) are not at all the concern of the Raqqa Civil Council and the tribal leaders, and they cannot be pardoned".

"Those who have surrendered are only Syrians, and they number a total of 275 including their families."

The US-led coalition had on Saturday announced a convoy would leave the city, specifying that it would not include foreign IS militants.

"We're very adamant about not allowing foreign fighters to leave the city," coalition spokesman Colonel Ryan Dillon told AFP on Sunday.

"Our stance was they either stay and fight or they surrender unconditionally."

"The last thing we want is foreign fighters to go free so they can return to their countries of origin and cause more terror and more havoc," he added.

But Dillon said local officials had not been asked for guarantees.

"This is a local solution," he said.

"While we may not fully agree with our partners sometimes, we have to respect their own solutions to their issues."

IS captured Raqqa in 2014, and under its rule the city become synonymous with the militant group's worst abuses and was transformed into a planning centre for attacks abroad.

The loss of Raqqa would be only the latest blow for IS, which has suffered a string of setbacks in recent months.

It was driven from its largest Iraqi stronghold Mosul in July and now holds only a sliver of territory in the country.

In Syria, its presence is largely confined to the eastern province of Deir Ezzor, where it is under attack by both the SDF and a Russia-backed Syrian government campaign.

On Saturday, Syria's army seized the former IS stronghold of Mayadeen in Deir Ezzor.