MAJURO, Marshall Islands (AFP) - Pacific castaway Jose Salvador Alvarenga departed the Marshall Islands on a Honolulu-bound flight on Monday to begin his journey home to El Salvador, an AFP reporter at the scene said.

Mr Alvarenga, who says he spent 13 months adrift in the Pacific, thanked Marshalls President Christopher Loeak for the support he had received after washing ashore 12 days ago before he boarded the United Airlines flight.

"Thank you for everything the people of the Marshall Islands have done for me during my stay," the 37-year-old fisherman said through an interpreter as Mr Loeak placed a woven lei garland around his neck.

Mr Alvarenga will arrive in Hawaii in the early hours of Tuesday and then travel to El Salvador, most likely via the US West Coast, to be reunited with the family who had long thought he was dead.

It will be a quicker and more comfortable journey across the Pacific than the 12,500-kilometre odyssey which began when a fishing trip off the Mexican coast went awry in late 2012.

A crewmate of Mr Alvarenga's - named as 24-year-old Ezequiel Cordoba - died during the journey because he could not survive on the diet of raw fish and turtle blood.