Fifteen of his former students are said to have been directly involved in acts of terror across the region.
Asked if he was embarrassed by this, Bashir said: "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."
One of those former students is Nur Said, who many thought was one of the hotel suicide bombers. While DNA tests from the bombers' bodies at both sites have ruled him out, there remains a view that he may have been Noordin Top's second-in-command in the operation.
In the little hillside village of Katekan, northwest of Jogjakarta, famed for its tobacco, a media crew said it had been staking out Nur Said's parents' home for days but they had gone into hiding.
Bashir said he had never met Nur Said.
Speaking within the grounds of the al-Mukmin school, where students studied a noticeboard with newspaper accounts of the attacks, Bashir was asked whether Noordin Top, who used the school as his main recruitment ground, should be apprehended.
"If Noordin M.Top has bad intentions, then he should be apprehended," said Bashir. "If he is right, then Allah will protect him. What I know about Noordin M.Top is that he is a Malaysian who fights to defend Islam."
Bashir claimed it was not Muslim terrorists who conducted the suicide bombings. "The person who bombed the Marriott is probably influenced by the CIA, which is an enemy of Islam. It will do anything to discredit and destroy Islam in Indonesia.
"In my opinion, acts of bombing are only allowed after one declares war against infidels. Such as al-Qa'ida, which has declared war on America. Go ahead (and bomb).
"I'm not saying the (Marriott and Ritz) bombers are wrong, they could have been right." But he would prefer if there was a formal declaration of jihad before targets were attacked.
Students and teachers call Bashir "Pak Ustad", meaning senior teacher. One teacher, Syehuddin, said he had no problem with the school's record of producing terrorists.
"Even though terrorists radiated from here, they also come from other places. Foreign intervention leads to all the attention on this school."
The school previously ran to university level but has since dropped off. Syehuddin would not say why this was, but it seems an al-Mukmin degree is no longer regarded as something you'd want on your CV.
Teachers claim they teach the origins of the various interpretations of the Koran and let students decide for themselves.
Bashir, who lives within the school grounds, said: "The connections between al-Mukmin and the Marriott bombing is just an allegation.
"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."
The Australian