The Indonesian Government has implicated one of the terrorists involved in the 2004 bombing of the Australian embassy in January's deadly Jakarta terrorist attack.

Indonesia's most senior minister after the President made the revelation as Indonesia continues to make raids and arrests linked to the attack on January 14, which left eight people dead.

Iwan Darmawan, also known as Rois, has now been isolated, but it is further confirmation that the attack was planned behind prison walls.

The terrorist has been on death row in Nusa Kambangan prison for more than a decade.

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During that time he has successfully held off the firing squad, because he still has the option of a judicial review.

In September 2005, he was sentenced to death for his role in the Australian embassy bombing.

In 2004, a 1 tonne car bomb exploded outside the Australian embassy in Jakarta, killing nine people including the suicide bomber, and wounding 150 others.

Rois bought the van and other materials used in the attack.

"In 2014 the attorney-general asked Rois whether he wanted his last legal challenge," Indonesian counter-terrorism analyst Adhe Bhakti said.

"He said he would launch a review, so that postponed the execution plans."

Indonesia's most security minister, Luhut Panjaitan, has now linked Rois to the January terrorist attack in Jakarta.

"We got information that there was a call from Nusa Kambangan to Bahrun Niam," he said.

Barun Niam is an Indonesian Islamic State (IS) leader in Syria, who has also been linked to staunch IS supporter Aman Abdurrahman.

Abdurrahman is in Nusa Kambangan prison and is also linked to the attack.

"Rois and Aman Abdurrahman are sharing the same cell with six to eight other people so they communicate intensely," Adhe Bhakti said.

Indonesia plays down Australia's travel alert

A spokesman from Indonesia's Correction Facilities, Akbar Prabowo, has acknowledged the flaws in prison system.

"What's happened is a lesson for all of us," he said.

"We need to make some improvements in regards to capacity, quality and supervision, especially for terrorism inmates."

Some of those changes have already been made, with the Indonesian Government isolating the most radical inmates, including Abu Bakar Bashir.

The Indonesian Government has played down Australia's latest travel alert, which warns a terrorist attack is the advance stages of planning.

It said there is no evidence of that.