Megumi Yokota who was only 13 years old when she was kidnapped by North Korean agents in 1977 on her way home from school.
The secretive state insists that Yokota killed herself in 1994, an explanation that Tokyo has long refused to accept.
Yokota's parents - father Shigeru, 81, and mother Sakie, 78 - spent five days last week with their granddaughter, 26-year-old Kim Eun-Gyong, and her family in the Mongolian capital Ulan Bator, Japan's foreign ministry said yesterday.
"We had hoped to meet her as a family... It was a pleasing and wonderful moment."
Also Read
Yokota became a symbol of a bitter bilateral row over Pyongyang's abduction of Japanese nationals in the 1970s and 1980s, mainly aimed at training North Korean spies in Japanese language and customs.
Pyongyang admitted in 2002 that it abducted about a dozen Japanese nationals over the two decades, and said eight of them had died, a claim rejected by Tokyo.
"We had seen her (Kim) many times on television, but it was the first time to meet her in person," he said.
The elderly couple said they did not ask about the fate of their daughter Megumi. Japan's Jiji Press news agency reported yesterday that Kim reiterated to the Yokotas that her mother was dead.
The couple had previously refused to meet Kim for fear of being used as a propaganda tool by Pyongyang to establish their daughter's death as fact.
"We did not want to make the meeting with her (Kim) anything that involves political matters," the abducted woman's mother said today. "She has grown up in that country. We weren't sure how much of the truth she could tell us."
Japanese Prime Minister Shinzo Abe, who has long championed to solve the kidnapping issue by taking a hawkish policy against the secretive state, said he was "moved" by news of the meeting.