But Kyodo news agency cited Song Il Ho, North Korea's ambassador to the discussions, as saying that both countries had agreed during Wednesday's meeting to keep talking and try to hold another round soon.
The talks to normalise bilateral diplomatic relations hinge on the abductions and Tokyo is also keen to bring North Korea back to the negotiating table over its nuclear programme.
North Korea has admitted kidnapping 13 Japanese citizens in the 1970s and 1980s during spy training and says eight of the 13 are dead, but Japan wants more information about the eight and another three it says were abducted.
Tokyo said there had been no progress on the issue.
Shinzo Abe, Japan's most senior government spokesman, told a news conference in Tokyo: "The other side has not responded to any of our requests regarding the abduction issue, so it is highly regrettable."
Asked whether Japan would increase pressure on North Korea as a result, Abe said Tokyo would not close the door on dialogue but said that talks must produce results.
"Our objective is not to merely hold talks," he said. "We want to seek a solution to the abduction issue through them."
"The other side has not responded to any of our requests regarding the abduction issue, so it is highly regrettable"
Shinzo Abe, Japan's chief government spokesman
But Abe criticised Pyongyang's demand to hand over Japanese members of non-governmental groups helping defectors leave the North.
"Their demand is outrageous. Making such a demand in itself would result in international criticism over North Korea's human rights policy," he said.
North Korea has said more than once it cannot return to the six-party nuclear talks, which group the two Koreas, Japan, Russia, the United States and China, unless the United States drops sanctions.