The Indonesian government has lifted its threat to ban the encrypted messaging app Telegram, saying it has taken steps to block "negative" content that includes forums for ISIL supporters.

Rudiantara, the minister of communications and information technology, met Telegram co-founder Pavel Durov on Tuesday, announcing that "we have agreed to keep Telegram accessible".

Earlier in July, the ministry said it was preparing to shut down Telegram in Indonesia, where it has several million users, if it did not develop procedures to block unlawful content including group discussions supportive of the Islamic State of Iraq and Levant (ISIL).

As a partial measure, it asked internet companies to block access to 11 addresses offering the web version of Telegram, saying it had several forums that were "full of radical and terrorist propaganda".

At a joint news conference with the minister, Durov apologised for failing to quickly respond to the Indonesian government's request, blaming a miscommunication.

READ MORE: Telegram blocks 'terror' content after Indonesia threat

He said there would be a line of direct communication between the ministry and top people in Telegram as that would allow it to shut down public channels "more efficiently within several hours".

"We have discussed ways to block publicly available propaganda of terrorism on Telegram, which is something we have committed to do globally, and particularly in Indonesia," Durov said.

The Indonesian government had not made any requests that would require Telegram's encryption to be compromised, he said, adding: "The basis of Telegram is a 100 percent promise of encryption. This is why our company exists."

Rudiantara said the blocking measures against Telegram could be lifted next week, but warned that other sites could now face scrutiny.

Many other social media sites, messaging apps and file and video-sharing systems are used in Indonesia, he said, specifically mentioning Facebook and Google as platforms that could be scrutinised in the "near future".

Suspected fighters 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 ISIL in Syria accused of orchestrating several attacks over the past 18 months.

Critics of the government's threat said it would make more sense to monitor the ISIL discussion groups for possible intelligence than to ban the app.

Several governments, including those of Australia and Britain, have urged technology companies to do more to help security agencies to thwart threats.