"The UN and other humanitarian organizations have called for help," Nobutaka Machimura said. "In view of the distress caused by the recent natural disaster, surely we should not to tie everything to the problem of the abductees."
Recent flooding in North Korea killed hundreds of people, displaced some 300,000 and destroyed a sizeable portion of the country's crops at the height of the growing season.
South Korea quickly promised to send $7.5 million in emergency food and medical supplies and $40 million in construction and fuel aid, and international aid agencies have also stepped in.
However, Japan has maintained a moratorium on humanitarian aid to the secretive Communist state since 2004 over the issue of Japanese citizens abducted in the 1970s and 1980s by North Korean intelligence services.
Pyongyang has acknowledged that it kidnapped at least 13 Japanese nationals. Five were eventually repatriated, while the remaining eight reportedly died in the interim. The released abductees said they had been forced to train North Koreans to spy against Japan.
Japan has not accepted North Korean assertions that the matter is now closed, insisting that many more of its citizens remain unaccounted for.
The topic will be among the main items on the agenda at bilateral working group talks between Tokyo and Pyongyang September 5-6 in the Mongolian capital, Ulan Bator, as part of the six-party negotiations on North Korea's nuclear disarmament.
Machimura, who took over the post of foreign minister Monday following the defeat of Prime Minister Shinzo Abe's ruling Liberal Democratic Party in recent parliamentary elections, said the question of humanitarian aid to Pyongyang would be decided quickly.
