Mexico has deployed naval search teams and military aircraft to locate the Friendship and Tigger Moth, which were carrying at least nine crew members, the Mexican navy said. BBC reported.
The vessels had been expected to arrive in the Cuban capital, Havana, on Tuesday or Wednesday, but there had been no communication from them and no confirmation of their arrival, the navy said.
They are among several vessels that have sought to carry supplies to the island nation since the US imposed an oil blockade in January, prompting a chronic fuel shortage.
The Mexican navy said it was committed to using all resources at its disposal to locate the boats and ensure the safety of the crews.
The two missing ships departed Isla Mujeres, in Mexico's easternmost state of Quintana Roo, on 20 March.
The nine crew members are from Poland, France, Cuba and the US. Mexico said it has established contact with maritime rescue co-ordination centres from each country along with their diplomatic representatives.
"The captains and crews are experienced sailors, and both vessels are equipped with appropriate safety systems and signalling equipment," the convoy's spokesperson told Reuters in a statement.
"We are co-operating fully with the authorities and remain confident in the crews' ability to reach Havana safely."
The captain of the Friendship, Adnaan Stumo, told the BBC they were "taking a whole bunch of aid, [a] bunch of solidarity activists, and we're sailing directly" in video messages as they were setting off.