Mr Hatoyama, Mr Lee and Mr Wen were holding talks in South Korea
The leaders of Japan, China and South Korea have said the sinking of a South Korean warship poses a threat to peace and stability in the region.
But China did not condemn North Korea over the incident, despite facing pressure from Seoul to take a stance.
South Korea says its ship, the Cheonan, was attacked by a torpedo from the North in March. Pyongyang denies the claim.
The comments ended three-day talks on Juju resort island in South Korea.
Tensions have been rising in the region since the Cheonan sank in March, with the loss of 46 sailors.
Chinese Premier Wen Jiabao said avoiding conflict between the Koreas was "most urgent", but did not apportion blame for the sinking of the Cheonan.
"The urgent task for the moment is to properly handle the serious impact caused by the Cheonan incident, gradually defuse tensions over it, and avoid possible conflicts," Mr Wen said.
"China will continue to work with every country through aggressive negotiations and co-operation to fulfill our mission of maintaining peace and stability in the region," he added.
‘Balance of power’
Beijing has refused to condemn North Korea, but has said it would assess the evidence objectively.
Japanese prime minister Yukio Hatoyama pledged support for the South Korean president and accepted the accusations against North Korea.
Japan has already said it is tightening its stringent sanctions against North Korea.
The three-nation summit was meant to focus on trade, but the sinking of the warship overshadowed other issues.
The BBC's John Sudworth in Seoul says the issue highlights the shifting balance of power in this region, most notably the change in China itself.
If China eventually accept North Korea's guilt, it may be a sign that it now sees it as more of a liability than an asset, our correspondent adds.
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