Charles Robert Jenkins, 64, landed at Jakarta's Sukarno-Hatta International Airport on a plane that Japan sent to North Korea to pick him up. Indonesia was chosen as a venue for the reunion because it has no extradition treaty with the United States, and it was considered safe from U.S. prosecution.
His wife, Hitomi Soga, buried her face in Jenkins' shoulder and embraced him. Soga then turned to her two teenage daughters and hugged them as Jenkins looked on with tears running down his face.
Abducted by North Korean spies in 1978, Soga had not seen her family since 2002, when North Korea allowed her to travel to Japan.
The family was taken by police escort to a Jakarta hotel, where toddlers gave them each a bouquet of tiger lilies. The eldest daughter, Mika, kissed one youngster on the cheek.
The family waved at 200 journalists camped out at the hotel.
"I'm very happy," said a smiling Jenkins, who wore a dark suit and tie and his white hair swept back. On his lapel was a pin bearing the image of Kim Il Sung, North Korea's founder.
Earlier, a North Korean TV broadcast in Japan showed Jenkins and his daughters before departure in Pyongyang wearing North Korean flag pins. He smoked a Marlboro cigarette - a luxury item in the impoverished state.
Jenkins was serving in a U.S-army unit based on the Demilitarized Zone between the two Koreas when he disappeared during a routine patrol in 1965. It is unclear whether Jenkins has spent any time outside North Korea since then.
He met and married Soga in 1980 in Pyongyang. Soga spent nearly a quarter-century in North Korea, before leader Kim Jong Il agreed with Japanese Prime Minister Junichiro Koizumi two years ago to allow her and four other kidnap victims to return home.
The U.S. government wants Jenkins to face charges that he deserted. The 64-year-old had refused to be reunited with his wife in Japan because of the possibility he could be extradited to stand trial in the United States.
It was unclear what would happen next for the family. Soga has said she will try to persuade her husband to join her in Japan, but he is reportedly still afraid of facing U.S. legal action and wants to return to North Korea.
By Lely T. Djuhari