Japan's change in tune came as a team of US nuclear experts arrived this week at North's main reactor complex in Yongbyon to begin disabling procedures.
The abductions of Japanese nationals by North Korean agents in the 1970s and 80s remains a main sticking point for both countries, which have no diplomatic ties.
North Korea says the issue has now been resolved, but Japan insists that several cases remain open and unexplained.
Japan also has sanctions in place after Pyongyang conducted its first-ever test of a nuclear weapon in October last year.
The February six-nation disarmament accord promises energy aid and political concessions in exchange if North Korea totally declares and disables all its nuclear programmes.
The North is also required to provide a complete accounting of its fissile material.
On Monday a team of US experts began the process of disabling the Yongbyon nuclear facility, the US state department said, but provided no further details.
Tom Casey, a spokesman, said the US team would continue working there until the disablement is completed.
The process is to disable three core facilities at Yongbyon - the reactor, the reprocessing plant and the fuel fabrication plant.
The US has said that once the nuclear plant is put beyond use it will also take steps to remove North Korea from its terrorism blacklist.