The power struggle on Anjouan has highlighted deep rivalries on the Indian Ocean archipelago, whose three main islands share a rotating national presidency but retain autonomy through local leadership under the terms of a 2001 peace deal.
The islands have seen 19 successful or attempted coups since independence in 1975.
The latest trouble began when Comoros' constitutional court said last week that Bacar's five-year term had expired, and ordered him to step down ahead of June elections.
Witnesses on Anjouan said on Friday that after two days of fighting, Bacar had regained complete control of the island, and his police had confiscated the arms and vehicles of a small government army contingent of about 30 soldiers.
Salim Miterand, a local photographer, said from Mutsamudu, Anjouan's capital: "Last night, police forces were driving round armed to the teeth. president Bacar wants to show the population he has won the battle."
Inhabitants said the shooting of previous days has subsided, but Anjouan locals were braced for more, as the national government considers sending reinforcements.
Abourahim Said Bacar, a government spokesman, said: "Mohamed Bacar risks plunging Anjouan into civil war. The government is deeply worried at the climate of terror he has imposed."
The spokesman said the house of Ahmed Abdullah Mohamed Sambi, the national president, who hails from Anjouan, had been ransacked by police there.
Anjouan's port and airport remained closed, while phone lines to local officials were cut.
In a further sign of widening instability across Comoros, Said Hamza, national military head, was deposed this week by his own officers, apparently for supporting Bacar.
The African Union has condemned Anjouan police for "seriously threatening the unity and national sovereignty of the Comoros".
First settled by Arab seafarers 1,000 years ago, and later a haven for pirates pillaging ships in the Indian Ocean, the rocky Comoros islands were annexed by France in 1904.
Since 1975, Comoros has been infamous for coups and coup attempts, four aided by Bob Denard, a French mercenary .
With a population of 670,000, the Comoros used to rely on exports of vanilla, cloves and ylang ylang oil.
But a slump in these commodities has left it increasingly dependent on remittances from abroad and donor aid.
Amid this week's chaos, some tourists continued sight-seeing in Anjouan.
Mohamed Said, a journalist, said :"I've seen tourists going round town without realising the dramatic events taking place around them."