Ma, who initiated the island's detente with former bitter rival China, will depart on August 11 for his seventh overseas visit since taking office in 2008, vice-foreign minister Simon Shen-yeaw Ko told a press conference.
Like his predecessor Chen Shui-bian of the China-sceptic Democratic Progressive Party during trips to Latin America and the Caribbean, Ma will make a transit stop in New York.
But unlike Chen who touted the US stopovers as "diplomatic triumphs" since Taiwan and the United States do not have diplomatic ties, Ma has tried to keep them low-profile.
Beijing protested to Washington whenever Chen, a high-profile advocate of independence, made transit stops in the United States.
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Beijing opposes any overseas visits by officials from Taiwan, which it still regards as part of its territory awaiting reunification.
The two sides split in 1949 at the end of a civil war.
Only 23 countries worldwide formally recognise Taipei instead of Beijing. Almost all of them are developing nations in Africa, Latin America and the Pacific.
And the diplomatic tug-of-war between the two former bitter foes has eased since Ma adopted a policy of not confronting Beijing. He was re-elected in January 2012.
Ma will attend the inauguration of Paraguay's president-elect Horacio Cartes on August 15. Paraguay is Taiwan's sole diplomatic ally in South America.
The trip will also take Ma to Haiti, Saint Christopher and Nevis, St Lucia and St Vincent and the Grenadines.
"The visit will help cement ties with our allies in the region," spokeswoman Li said.