According to Chinese officials, Wen told Shinzo Abe, the Japanese prime minister, that he should be careful in his handling of Japan’s wartime past and its occupation of much of East Asia before and during World War II.
"Through efforts of both sides, we overcame problems obstructing the development of relations," Wen told reporters after Sunday’s meeting.
"I am happy to see China-Japan relations moving forward," he said, but added: "Our problems are still not small."
"I am happy to see China-Japan relations moving forward. Our problems are still not small"
Relations between China and Japan cooled markedly under Abe's predecessor, Junichiro Koizumi, who regularly visited Tokyo's Yasukuni war shrine.
The shine honours Japan’s war dead, including several convicted war criminals, and visits there by Japanese leaders have often sparked criticism across Asia.
Ties have also been strained by territorial disputes and rival claims to natural resource areas.
Abe has not visited the shrine since taking office in September, although he has declined to expressly rule out any future visit.
Abe has made improving relations with China a priority of his administration and visited Beijing within weeks of being sworn in.
But he has also been vocal in criticising weapons sales to China and on Saturday he urged the European Union not to lift its arms-sales embargo against Beijing.
His moves to upgrade the status of Japan’s military and make the country more assertive on the international stage have also caused unease in China.
Japan meanwhile has its own worries about China’s growing clout in South-East Asia, seeing China as both a crucial market for its own exports and as a powerful competitor.