The Dalai Lama said last year he wanted to visit Taiwan in an interview with a local newspaper in the northern Indian city of Dharamsala, but the China-friendly Ma at the time said the timing was not right for such a visit.
Ma´s office attempted to play down the political significance of the visit when asked if it would impact ties with Beijing.
Beijing accuses the Dalai Lama of trying to split Tibet from China and reacts angrily to any country hosting him.
"The visit is based on humanitarian and religious considerations which should not hurt cross-strait ties," said presidential spokesman Wang Yu-chi.
The Dalai Lama was invited by seven mayors from the pro-independence opposition Democratic Progressive Party (DPP) to visit southern Kaohsiung county, which was devastated when Typhoon Morakot struck earlier this month.
In Beijing, China´s Taiwan Affairs Office declined to immediately comment on the Dalai Lama´s proposed visit.
The Dalai Lama had accepted the invitation, his spokesman Tenzin Taklha told AFP on Wednesday from Dharamsala, where his exiled government has been based since a failed Tibetan uprising against Chinese rule in 1959.
The Dalai Lama made a historic first trip to Taiwan in 1997 and visited the island again in 2001, triggering strong condemnation from China.
China and Taiwan split in 1949 after a civil war but Beijing still considers the island part of its territory awaiting reunification, by force if necessary.
Ties have improved dramatically since Ma took office last May pledging to boost trade and tourism with China, after eight years of strained relations under the DPP.
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