Ma, 57, urged both China and his country to start "a new chapter of peace" so there can be regional stability, the BBC reported.
Ma succeeds Chen Shui-bian, who had been strong supporter of Taiwan's independence.
With Ma taking over, Chen gave up his presidential immunity, prompting prosecutors to say they have begun a corruption inquiry against the former president, the report said. Chen and his wife have been accused in a $450,000 embezzlement case.
Ma, who represents the Taiwan Nationalist Party, also wants more dialogue with China.
"Seeking cross-strait peace and maintaining regional stability is our goal and Taiwan still strives to become a peacemaker in the world," he said.
China has always claimed the island nation as part of its territory. There have been growing global concerns over China's massive military buildup in recent years and its threat to Taiwan.
Vincent Siew, the new Taiwanese vice president, has met Chinese President Hu Jintao, the report said.
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