Comoran troops are still facing some resistance from supporters of a renegade officer despite taking all major towns on the island of Anjouan.
Officials say several of Mohamed Bacar's supporters have been killed since the African Union-backed invasion of Anjouan began at dawn on Tuesday.
Col Bacar's whereabouts are unclear amid rumours he may have tried to flee dressed as a woman.
Comoros declared his re-election as island president in July to be illegal.
The AU also condemned Mr Bacar's move and agreed last month to deploy around 1,500 troops in support of the federal President, Ahmed Abdallah Sambi.
About 450 Comoran and AU troops landed in an amphibious assault as dawn broke on Tuesday.
The invading force soon captured the airport at Ouani, the island's second town, Domoni, and the main town, Mutsamudu.
Residents of the island were pictured greeting the government forces with jubilation as they patrolled the streets.
The presidential palace outside the town was found abandoned.
Sentry posts were empty and the building's doors wide open, according to reports.
'Disguised as a woman'
Despite the ease with which the troops seized control of the major towns, acting Defence Minister Bacar Dossar said they had not yet secured total control of Anjouan.
The Comoran army was supported by African Union troops
They were, he said, "trying to flush out a pocket near [Col Bacar's] residence in Barakani".
Mr Dossar said the precise whereabouts of the rebel leader remained unclear and that he was still being sought by government troops.
The minister also refused to confirm persistent reports that Col Bacar has tried to avoid capture and reach the nearby French-administered island of Mayotte by dressing as a woman.
"I think those are rumours," he told Radio France Internationale.
"A serious search has to be carried out and I think that will be possible starting tomorrow, as we take control of the whole island."
Mr Dossar said several members of Col Bacar's Gendarmerie Forces had been arrested. They included three "three high-ranking officers", one army source told the Associated Press.
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.
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