Taiwan says its leader made a transit stop in India on his way to Africa. India has previously banned the island's top officials from visiting.
Taiwan's foreign ministry said on Monday that the weekend stop was for no other purposes than fueling. It said it had kept President Ma Ying-jeou's stop in Mumbai secret because of the event's sensitivity.
India has diplomatic ties with Beijing, not Taipei. The two sides split amid civil war in 1949.
Beijing claims the self-ruled, democratic island as its territory.
The foreign ministry said Ma was allowed to refuel partly because of warming relations between Taiwan and China.
Ma's predecessor Chen Shui-bian would trumpet his overseas visits as diplomatic victories to the ire of Beijing.