Indonesian lawmakers also demanded the country's sovereignty be defended as anger mounted at the map of the under-construction "Funtasy Island".
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The map initially showed Pulau Manis -- islets that make up the resort -- in blue, the same colour as Singapore, prompting outrage in Indonesian media at what they said was an attempt to claim their country's territory by stealth.
Both governments scrambled to defuse the escalating anger, with the city-state's foreign ministry saying it was "deeply puzzled" since it did not claim the islands while Jakarta insisted it was a mistake.
Pulau Manis was also changed to red on the website map, one of the colours on the Indonesian flag.
But by this point, Indonesian army and navy personnel had already been dispatched from a local base to the resort to place the country's flag on the highest point of one of the islands.
Local tourism chief Guntur Sakti said he had sent a warning to Singapore over the map, while Indonesian parliament speaker Ade Komaruddin told news website Tribunnews that "our sovereignty must be upheld".
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However Indonesian foreign ministry spokesman Arrmanatha Nasir played down the row, saying it was due to a mistake by the group Funtasy Island Development, which is building the resort.
"The issue has basically been resolved," he said. "The mistake has been corrected".
Funtasy Island Development did not respond to a request for comment.
The affluent city-state and its huge neighbour have a historically acrimonious relationship. They clashed repeatedly last year after Indonesian forest fires choked Singapore with toxic smog for weeks.
The Funtasy Island website describes the development, which is 16 kilometres (10 miles) from Singapore, as the world's biggest eco park, where visitors can stay in villas and enjoy nature trails and water sports.
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