The meeting in Tokyo among officials comes ahead of trilateral talks with South Korea on Saturday.
The last round of talks was in 2011, before ties worsened over a row over islands in the East China Sea.
China also claims Japan has failed to adequately atone for aggression in World War Two.
But the BBC's Celia Hatton in Beijing says relations are slowly improving and at the top of the meeting's agenda is the establishment of a maritime communication hotline.
There have been fears that a clash - accidental or otherwise - between Chinese and Japanese paramilitary vessels patrolling waters around the disputed islands, known as Senkaku in Japan and Diaoyu in China, could trigger a conflict.
Japan's deputy foreign minister told reporters that both sides hoped to "especially discuss intentions and thoughts behind each other's defence policy."
His counterpart, China's Assistant Foreign Minister Liu Jianchao, said that China hoped that the two countries "would develop a mind to face history squarely and look into the future".
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