The Comoros' vice-president has been appointed head of Anjouan island as federal troops continue to search for its renegade leader Mohammed Bacar.
"Ikililou Dhoinine will be the political authority in Anjouan until a transitional government is set up," a government spokesman told AFP.
Reports from Anjouan say gunfire can still be heard following Tuesday's Africa Union-backed dawn attack.
Comoros declared Mr Bacar's election as island president in July to be illegal.
Correspondents say both Mr Bacar's residence and office were deserted on Wednesday.
Mohammed Desara, the Comoran chief of staff for defence, said troops are 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.