Jose Salvador Alvarenga, 37, arrived in his native El Salvador to a media throng, a daughter who did not remember him and a mother who thought he was dead.
Mr Alvarenga was taken in a wheelchair before a crush of more than 100 mostly foreign journalists, intending to speak.
But when ForeignMinister Jaime Miranda handed him the microphone, he held it in silence. Then he put his hands to his face and appeared to cry.
Mr Miranda told the crowd: "We ask for your understanding. He's had a very exhausting trip."
Mr Alvarenga was thought to be heading to a local hospital for tests before returning to his home village of Garita Palmera.
His story stunned the world when he washed up on the Ebon atoll almost two weeks ago, appearing robust and barely sunburned after more than a year at sea drifting from Mexico to the Marshall Islands.
The journey back home after a week of rest and medical treatment was marked by long stays in Honolulu and Los Angeles, where doctors checked his health.
Emma Alvarenga, an aunt who arrived at the airport to see him but was left outside the VIP lounge where he was taken, said: "I'm so happy to know he's alive, that he returned. I want to give him a hug."
His father, Jose Ricardo Orellana, 65, who owns a store and flour mill, said his son first went to sea at 14, adding: "The sea was his thing."
The castaway's 14-year-old daughter Fatima had made an archway of palms for the front door of the family home and a sign saying Welcome.
She didn't remember ever seeing her father, who left El Salvador to make a living fishing in Mexico when she was just over a year old.
Mr Alvarenga's story of drifting across 6500 miles of open ocean, eating raw fish, turtles and drinking bird blood to survive initially left many sceptics but experts said it would have been possible for him to survive.