The federal government of the Union of Comoros has refused to recognise Bacar's re-election as the island's president last June and vowed to remove him.
Each of the three main islands in this Indian Ocean archipelago has a regional president. The country's main leadership, including Ahmed Abdallah Sambi, the president, is based in Moroni, on the main island of Grand Comore.
"I have ordered the Comoran army and the the forces of our country's friends to bring Anjouan back under the rule of law and free her citizens," Sambi said on Monday, adding that he did so "without joy, like swallowing a bitter pill".
The fleet set sail as the central government used helicopters to drop leaflets on Anjouan warning of the coming assault and telling civilians to stay in their homes.
The National Development Army "informs all the residents of Anjouan that it will be in Anjouan within days or in the coming hours," the leaflets said.
The Indian archipelago nation consists of three islands: Grand Comore, Moheli and Anjouan
Each island has its own president and administrative authorities
The Union of Comoros central government is led by President Ahmed Abdallah Sambi
Anjouan is home to about 300,000 of the archipelago's 700,000 population
The country has seen 19 coups or attempted coups since independence from France in 1975
Idi Nadhoim, the Comoran vice president, said: "Colonel Bacar will be arrested if he does not flee and will face Comoran courts for treason, usurpation of power, torture and war crimes, as documented by complaints which Anjouanese victims have filed."
On Sunday, the AU troops sent to the Indian Ocean island nation practised beach landings for the operation named Democracy in Comoros.
An Anjouan minister told the AFP news agency that Bacar's troops were ready to face the government forces.
"We have heard on the radio that AU troops and forces loyal to Comoran President Ahmed Abdallah Sambi started moving," Mohamed Abdou Madi, one of Bacar's aides, said.
"They have decided to kill, but we are not afraid. We are well prepared. Our forces are ready and it's going to work."
Bacar is believed to have about 300 soldiers.
The government has accused Bacar of planning to break away from the union, but the Anjouan leader insists he wants only greater autonomy rather than full independence.
Last Thursday, he told the AFP news agency: "I am still determined to defend Anjouan despite my concern that people are ready to come here and fire on the Anjouanese. But I am continuing with my preparations to defend Anjouan."
The archipelago has survived 19 coups or coup attempts since it acquired independence from France in 1975.