Details of the crash remain sketchy but officials from Yemenia said some bodies had been recovered from the site.
The plane carrying mostly French and Comoran nationals was flying from the Yemeni capital, Sanaa, to Moroni on the main Comoros island of Grande Comore.
Ibrahim Kassim, an official with the regional air security body Asecna, said search and rescue planes had spotted debris at the supposed crash site.
He said the plane had probably come down 5-10km from the coast and believed that it crashed along its landing approach.
"The weather is really not very favourable. The sea is very rough," Kassim told Reuters.
Asecna, or the Agency for Aviation Security and Navigation in Africa and Madagascar, covers Francophone Africa.
Moroni airport authorities said civilian and military rescue teams were immediately deployed to search for the plane in the rough waters.
"Two French military aircraft have left from the islands of Mayotte and Reunion to search the identified zone, and a French vessel has left Mayotte," Hadji Madi Ali, the director-general of the airport, said.
|The aircraft came down in stormy weather as it tried to land early on Tuesday [AFP]
Mohammad al-Sumairi, deputy general manager for Yemenia operations, told Reuters that they did not know the cause of the crash or have any information on survivors.
"The weather conditions were rough, strong wind and high seas. The wind speed recorded on land at the airport was 61km an hour," he said, adding there could be "other factors".
Comoros officials said the plane could have crashed in the area of Mitsamiouli, a town on the main island.
Hamid Bourhane, the interior minister, told Reuters the army had sent small speedboats to the suspected crash site.
"At the moment we don't have any information about whether there are any survivors," he added.
The Comoros covers three small volcanic islands, Grande Comore, Anjouan and Moheli, in the Mozambique channel about 300km northwest of Madagascar and about the same distance east of the African mainland.
This is the second Airbus to plunge into the sea this month, after an Air France Airbus A330-200 crashed into the Atlantic Ocean killing 228 people on board on June 1.
In 1996, a hijacked Ethiopian Airlines Boeing 767 also crashed into the sea off the Comoros islands in 1996, killing 125 of 175 passengers and crew.