Comoros police said on Monday that only 22 survivors have been found so far.
Roland Andreas, director of investigations at the state secretariat for public security, said that the Comoros-flagged 'Al-Mubarak' left the Madagascan port of Mahajanga on Friday but had not arrived in the Comorian capital of Moroni on Monday.
A senior official at the Comorian transport ministry told Reuters that the ship had been due to arrive in Moroni on Saturday.
Andreas said: "We lost contact with the boat when it was between the islands of Moheli and Mayotte."
He added that 17 of the passengers were Malagasy citizens.
French sailors based on the nearby island of Mayotte, requested to help by the Comorian government, found one survivor before rescuing a further 21 from a lifeboat.
They then found another lifeboat but it was not clear how many people were in it.
The type of ship and the reason for its loss were not immediately known.