"The global economic crisis has started to have an impact," said Sapta Nirwandar, director-general for marketing at the Culture and Tourism Ministry.
"With the looming crisis, I'm afraid we will not have the expected peak of foreign tourist arrivals in December," Nirwandar said, referring to the usual end-of-the-year surge of tourists to the tropical isles.
Despite record-breaking tourism numbers at Indonesia's prime beach resort of Bali, the country will again miss this year's overall target for foreign visitors, he predicted.
Due to the global economic downturn, the government has revised down its targets for 2008 foreign tourist arrivals to "realistic figures" of around 6.4 million, from initial goal of 7 million.
According to the National Statistics Agency, the three quarters spanning January to September brought nearly 4.6 million tourists, a 12.2 per cent increase from the same period of 2007, or 4.1 million.
Indonesia's tourism industry has been hit by a string of calamities over the past five years, ranging from bomb attacks in Bali and Jakarta, to tsunamis and earthquakes, and outbreaks of bird flu and SARS respiratory disease.
Travel warnings issued by several countries have also taken a toll.
2008 began on good footing, until the latest catastrophe - the financial meltdown in the US and Europe - struck.
"Bali this year had a record number of arrivals and was projected to have its strongest year ever, until the recent financial situation, and we have also been impacted by the recent executions of the Bali bombers," said Darryl Marsden, general manager of the Hard Rock Hotel Bali.
Bali hotels are reportedly enjoying 90 per cent occupancy rates this November and December.
Bali, the gem of Indonesia's tourism industry, was hard hit by the 2003 bombings that killed up to 200 people, many of them Australian tourists, followed by another suicide bombing in 2005.
"The outlook for Bali's tourism industry remains positive," Ida Bagus Ngurah Wijaya, head of the Bali's tourism board, told Deutsche Presse-Agentur dpa. "The main issue in Bali is security. As long as security is being guaranteed, there will be more and more foreign visitors to Bali in 2009."
But no one knows to what extent the financial crisis will impact the island.
The sprawling nation of more than 17,000 tropical islands, teeming with coral reefs, exotic wildlife, volcanoes and inland waterways, is a nature lover's paradise.
Istijab Danunegoro, chairman of the Indonesian Hotel and Restaurant Association chapter in Yogyakarta, the Javanese cultural capital that is another prime tourist destination, foresees a slowdown in arrivals next year but still predicts growth.
"With a better cooperation among related parties and better promotion, the outlook for tourism remains positive," Istijab said, projecting tourist arrivals to increase by about 10 per cent in 2009.
Cultural and Tourism Minister Jero Wacik has also called for greater cooperation within the sector, given its huge capacity to create employment and reduce poverty.
"This industry needs interactive efforts between all parties concerned - the government, tourist players as well as the public," Wacik told the Indonesian daily Kompas.
He acknowledged that the country is losing some tourists to neighbouring countries, partly because of limited promotion funds, inadequate transport and infrastructure, and a lack of professional guides."Domestic airlines have so far still been unable to cover the requirement of transporting tourists to the destinations," the tourism minister said. "Moreover, when the Visit Indonesia program again rolled out this year, not many domestic airlines and hotel operators welcomed this."