Japanese prime minister Shinzo Abe said he was satisfied the committee has the mandate to carry out a serious investigation into the abductions, although previous deals with the North have fallen through.
Japan will continue to abide by UN sanctions on North Korea over its nuclear and missile programmes.
Mr Abe said: "This is only a start. We are determined to do everything we can, with a renewed effort, towards a comprehensive resolution."
His decision is due to be formally approved by his cabinet today.
The announcement follows a meeting between North Korean and Japanese negotiators in Beijing earlier this week.