The fugitive rebel leader of the Comoran island Anjouan is reported to be on the French-run island of Mayotte.
The French government confirmed that Colonel Mohamed Bacar had requested political asylum in France.
On Tuesday, federal troops and an African Union force launched an operation to retake the island from Colonel Bacar's rebels.
The operation followed Colonel Bacar's refusal to step down after disputed elections last July.
The island of Mayotte is the only one of the Comoros islands to have opted to remain French when the other islands gained independence - but it remains a source of contention with both countries claiming sovereignty.
The BBC's Jonny Hogg says Colonel Bacar's arrival on the island follows reports last week that he had received backing from individuals on Mayotte during the eight-month political stand-off.
The government in the Comoros has expressed disappointment that he was able to flee to Mayotte.
A government spokesman warned that if Colonel Bacar was not returned to face justice it could cause a diplomatic crisis.
Earlier on Wednesday, the Comoros authorities appointed a new transitional leader for Anjouan - the vice-president of the Comoros, Ikililou Dhoinine.
"Ikililou Dhoinine will be the political authority in Anjouan until a transitional government is set up," a government spokesman told AFP.
Comoros declared Mr Bacar's election as island president in July to be illegal.
Mohammed Desara, the Comoran chief of staff for defence, said troops were continuing to pursue elements loyal to Mr Bacar and secure the island fully.
It is not known how many people died in the fighting but Mr Desara said it was certain that at least some of Mr Bacar's fighters had been killed.
Government spokesman Abdourahim Said Bakar said a transitional government would be set up by the end of the week and Mr Ikililou was already on his way to Mutsamudu, the island's capital.
About 600 Comoran and AU troops landed in an amphibious assault as dawn broke on Tuesday.
Residents of the island were pictured greeting the government forces with jubilation as they patrolled the streets.
The Comoros archipelago in the Indian Ocean has had a fractious history since independence from France in 1975, experiencing more than 20 coups or attempted coups.
The three main islands of the archipelago - Grand Comore, Moheli and Anjouan - lie 300km (186 miles) off Africa's east coast north of Madagascar.