Japan is expected to push for a reopening of the investigation into the fate of the abductees, kidnapped in the 1970s and 1980s to train North Korean spies.
The issue, a hugely emotional one in Japan, was already brought up in an earlier bilateral meeting held in China in March.
Japan is said to have previously told the North Korean head negotiator, Song Il Ho, that it is willing to lift some economic sanctions if there is evidence that Pyongyang is making a serious effort to investigate the case, Kyodo News said citing unnamed sources.
Other issues that are thought to be on the agenda are the North Korean hermit state's missile and nuclear weapons programmes, but the delegations have remained tightlipped so far.
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"We had intense, serious and frank discussions," Japanese chief delegate Junichi Ihara, director general of the foreign ministry's Asian and Oceanian Affairs Bureau, said at a press conference yesterday after the first day of talks.
He added that "as only the first day is over, I'd like to refrain from making comments that could give any prejudgement over the course of the talks."