Research in Motion, the Canada-based manufacturer of the popular BlackBerry communications device, faces growing trouble that appear to be coming to a head from government regulators in Indonesia, its second-biggest global market.

The Indonesian Telecommunications Regulatory Body is threatening to cut off RIM’s internet access after the company said it would establish its data center in Singapore rather than Indonesia.

The Ministry of Communications and Information Technology has the final say. Titaful Sembiring, the head of the communications ministry, said Tuesday that the government would issue a regulation requiring all telecoms companies operating in the country to house their servers domestically, a shot particularly aimed at BlackBerry. The regulation is likely to be completed in January, he said.

RIM has faced problems in other countries in Asia as well over question about the confidentiality of messages. It has been in complex negotiations for months with the government of India over access to messages and has faced threats in Saudi Arabia, Malaysia and other countries although there has been no concrete action. Even the United Kingdom has threatened action after mobs were thought to be communicating by smartphones in riots earlier this year.

India in particular has threatened BlackBerry’s operations because of what the government regards as the threat of terrorists being able to use the devices to transmit confidential messages between them. BlackBerry smartphones were found in the rucksacks of the terrorists who shot up Mumbai in November of 2008, killing 166 and wounding more than 200.

RIM has repeatedly argued that only the customers have the keys to unlock their devices.