Radio Comoros broadcast a statement by Army Chief of General Staff Assoumani Azzali that said President Tadjiddine Ben Said Massonde had been removed from power. He and other government officials had been asked to remain in their homes.
There were no immediate reports of violence on the archipelago.
"The army has taken over to prevent our country from being plunged into chaos. We cannot sit and wait for it to collapse," said the statement. The radio also played martial music.
The army announcement marked the fourth coup in the Comoros since the country gained independence from France in 1975.
The country of 700,000 people is located 190 miles east of the coast of Mozambique and is made up of Grand Comore, Moheli and the secessionist island of Anjouan.
Claiming Anjouan was being cut off from national revenues brought in by the export of cloves, vanilla and ylang-ylang flowers for perfume, its leaders first tried to become a French overseas territory like neighboring Mayotte island. But when France turned that down, they opted for independence.
The government of former President Mohamed Taki Abdulkarim sent in troops to put down the secession, but they failed. Thousands of Anjouan residents have fled to the main island since the fighting broke out.
Army spokesman Lt. Rashidi Abdullah said Friday from the main island that under military rule, anyone found harassing people from Anjouan would be severely punished.
"We do not want the Anjouan people to leave," Abdullah said.
A peace conference held in Madagascar to resolve the Anjouan conflict ended last week with little progress. The Anjouan delegation put off signing a framework agreement worked out by the Organization of African Unity, pending consultations with colleagues at home.
Under the OAU-backed agreement -- signed by representatives of Grand Comore, Moheli and the Comoros government -- each of the three islands would have its own government within a new entity to be called the Union of Comorian Islands, which would have a separate administration.
When the outcome of the conference became known, gangs in Grand Comore began harassing people from Anjouan and forcing them to leave on boats to return to their home island.
Tadjiddine took power after President Mohamed Taki Abdulkarim died Nov. 6. Tadjiddine indefinitely postponed presidential elections scheduled for February.
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