He was convicted - and subsequently cleared - of inciting terror in relation to the Bali bombings of 2002.
Bashir has always denied being the spiritual head of JI.
The group is believed to be responsible for the Bali attacks.
"This [terror] will not end until the government follows the right path," he said.
Asked by The Australian whether he felt any sadness for the victims of the attacks, Bashir said: "What makes me sad about the bombings was that it involved innocent people being killed.
"People such as women and children who are not involved in the fight against Muslims should not be killed.
"But the problem is we don't know for sure that the victims weren't involved in the fight against Islam. Even the thought of fighting against Islam is involvement. Everyone that thinks like that is allowed to be killed."
Around 2,000 students attend the al-Mukmin religious school he co-founded and 15 of his former students are said to have been involved in terror activities across Indonesia.
However, Bashir denied links to his school and last week's bombings.
"The connections between al-Mukmin and the Marriott bombing is just an allegation," he said.
'No Muslim terrorists'
|Fifteen students from Bashir's school have allegedly been involved in terror activities[AFP]
He also denied the existence of terror suspects belonging to the Muslim faith.
"There are no Muslim terrorists. The terrorists are the CIA, the Americans and the Australians. They're the ones who terrorise Muslims.
"The Australians are making a fuss about their victims, but when it comes to Muslim victims they don't say anything about it."
Bashir also said that he did not know enough about Noordin Mohammed Top, said to head the JI splinter group accused of planning the Jakarta attacks.
"If Noordin Top has bad intentions, then he should be apprehended," Bashir said.
"If he is right, then Allah will protect him. What I know about [him] is that he is a Malaysian who fights to defend Islam."
Bashir believes foreign influence in Indonesia, particularly from the United States, has resulted in continued instability, and believes "the Islamic way" will serve as a solution.
"My war is to promote Islam through preaching. God willing, if the [Indonesian] government can return to the Islamic way, we can fight the Americans because those kafirs [non-Muslims] are weak. God willing, the jihadists will prevail."