Dispatch of the mission is part of an accord made last week by the the two countries, Chief Cabinet Secretary Yoshihide Suga said.
Japan and North Korea have no diplomatic ties and they contact each other through their embassies in Beijing at present.
Since North Korea in 2008 agreed to reopen investigations but failed to keep its promise, Japan has been mulling ways to ensure an effective probe by the North.
"We strongly requested what had been missing in the previous 2008 accord -- such as meeting people concerned and visiting relevant places while staying there -- and it has been accepted," Suga said in a programme on public broadcaster NHK.
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Initially the officials would stay there for short periods, but Tokyo is considering making them resident officials and establishing a permanent office, the news agency said, quoting anonymous government sources.
The Japanese government said Thursday it would ease sanctions against North Korea if the secretive state delivers on a pledge to reinvestigate the cases of Japanese nationals kidnapped in the 1970s and 1980s to train spies.
The announcement, a major breakthrough in a very strained relationship, comes after three days of talks between the two sides in Sweden, and marks the most positive engagement between Pyongyang and the outside world in many months.
Tokyo has insisted that they were still alive and that there should be more kidnap victims from Japan.