Rudiantara, the Minister of Communications and Information Technology, who met Tuesday with Telegram co-founder Pavel Durov announced that "we have agreed to keep Telegram accessible."
Many other social media sites, messaging apps and file and video sharing systems are used Indonesia, he said, specifically mentioning Facebook and Google as platforms that could be scrutinized in the "near future."
Earlier this month, the ministry said it was preparing to shut down Telegram in Indonesia, where it has several million users, if it didn't develop procedures to block unlawful content including pro-Islamic State group discussion groups.
As a partial measure, it asked internet companies in the world's most populous Muslim nation to block access to 11 addresses offering the web version of Telegram. Durov apologized for failing to quickly respond to the Indonesian government's requests for apparent terror content to be blocked, blaming a miscommunication.
Rudiantara, who uses one name, said the ministry and Telegram will put in place standard operating procedures that improve the ability to "address the negative content in Telegram." The blocking measures against web Telegram could be lifted next week, he said.
Suspected militants arrested by Indonesian police have told authorities that they communicated with each other via Telegram and received orders and directions to carry out attacks through the app, including from Bahrun Naim, an Indonesian with the Islamic State group in Syria accused of orchestrating several attacks in the past 18 months.
Critics of the government's threat said it would make more sense to monitor the IS discussion groups for possible intelligence than banning the app.
Durov told reporters there would a line of direct communication between the ministry and top people in Telegram but also said he wouldn't have come to Indonesia if the government had made any requests that would require Telegram's encryption to be compromised.
"The basis of Telegram is a 100 percent promise of encryption. This is why our company exists," he said.
"We've discussed ways to block the public channels available for the propaganda of terrorism, which is something that we are committed to do globally, and particularly Indonesia," Durov said.
The free messaging service can be used as a smartphone app and on computers through a web interface or desktop messenger. Its strong encryption has contributed to its popularity with those concerned about privacy and secure communications in the digital era but also attracted militant groups and other criminal elements.
Durov said about 20,000 people sign up to use Telegram in Indonesia daily.