SAN JOSESAN JOSE (Reuters) - Costa Rica's civil aviation agency suspended local airline Nature Air on Friday, two weeks after one of its small planes crashed near a tourist beach, killing two Costa Rican pilots and 10 U.S. citizens.

Ennio Cubillo, director of the civil aviation agency, informed Nature Air in a letter that it "preventatively" suspended all operations because several key employees were no longer with the company.

"It doesn't directly have to do with the accident," said a civil aviation source who declined to be named because the investigation is still proceeding.

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Nature Air's pilot training director died in the crash on New Year's Eve near the Punta Islita beach town about 140 miles (230 km) west of the capital, San Jose. The co-pilot was also killed, along with a family of five from New York.

Nature Air's operations manager quit this week and its aerial security director has requested a leave of absence.

"Nature Air doesn't have, at the moment, a reliable and effective management structure to guarantee the execution of safe air operations," said the letter from Cubillo, who has said the investigation could take months.

Investigators are analyzing weather conditions at the time of the crash, possible mechanical failures and human error to determine what caused the Cessna 208B Grand Caravan to plummet from the sky shortly after takeoff.

Earlier this week, Costa Rican authorities raided Nature Air's offices in what they described as a routine operation to collect information.