Myunghee Bae met her son, being held on charges of attempting to topple the regime, at a hospital a day after she arrived in the reclusive communist state, Japan's Kyodo News agency reported.
He is said to be suffering serious health problems and to have lost more than 50 pounds (23 kilogrammes) since being jailed.
But Kyodo quoted his mother, known by her Korean name Song Myung-Hee, as saying her son "did not look that bad".
Bae, a 44-year-old tour operator also known by his Korean name Pae Jun-Ho, was arrested last November as he entered the northeastern port city of Rason.
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He was sentenced to 15 years hard labour on charges that he was trying to bring down the regime of its young leader, Kim Jong-Un.
Bae was transferred from a prison camp to a hospital in Pyongyang on August 5, said the Chosun Sinbo, a pro-Pyongyang newspaper published in Japan, which normally speaks for the regime in the North.
"My heart was broken into pieces when his prison interview was released on July 3 because his appearance was very shocking," she said.
"He looked so different and he lost so much weight. I could not believe that prisoner was my son."
North Korea, which strictly bans religious proselytising, has said Bae was a Christian evangelist who brought in "inflammatory" material.
US officials say Bae is now very sick, and have called for his release as a humanitarian gesture.
Bae was sentenced at a time of heightened military tensions on the Korean peninsula, leading to suggestions that Pyongyang hoped to use him as a diplomatic bargaining chip to extract concessions from Washington.