Madagascar's Port, Maritime, and River Authority (APMF) said the boats had set sail from Somalia for the French Indian Ocean territory of Mayotte on Nov. 2, a journey of several hundred kilometers, Reuters reported.
On Saturday, the port authority reported that local fishermen discovered the first boat drifting on Friday near Nosy Iranja. They rescued 25 people, including 10 men and 15 women, but seven occupants died, the authority said.
A second boat carrying 38 people arrived at Madagascar's Port du Cratère, according to APMF. The maritime authority did not disclose a death toll for the second boat but confirmed the rescue of 23 people.
Somali Information Minister Aweis, citing information from his counterparts in Madagascar, confirmed the total death toll at 22.
"They were about 70 Somalis, 22 of them died. One boat was carrying 38 people and the other boat was carrying 32 people," Aweis said on state-owned television late on Sunday.
In recent decades thousands of people have attempted to make the crossing to Mayotte, which has a higher standard of living and access to the French welfare system.
Mayotte is officially part of France, although Comoros claims it.
Aweis said Somalia will investigate where the boats sailed from, terming those who organized the trip as criminals involved in illicit immigration.
"This is also a message of warning to those who want to immigrate illegally before they go and die in such manner. It is unfortunate people still go despite danger," he added.
In early November, at least 25 people died off Comoros islands after traffickers capsized their boat.