The ministry also said later that 10 foreigners were passengers aboard the plane, which was flown by two Costa Rican pilots.
Punta Islita, on Costa Rica's Pacific Coast, is popular among North American and European tourists for its pristine beaches and lush landscape.
The U.S. State Department confirmed that "multiple U.S. citizens" died in the crash.
The plane crashed in a wooded area on Sunday. "We are in contact with Costa Rican aviation authorities and will continue to monitor the situation". The spokesperson would not confirm the nationalities of those on board.
Authorities said that so far they had only a list of passengers provided by the airline and were awaiting official confirmation of their identities.
Cubillo said the cause was under investigation. They said within minutes after takeoff the plane took a nose dive and crashed. "Our heart sank, we got some pain in our stomachs", Dawn Wolfe told ABC News. The other two killed are local crewmembers.