A Jakarta court ruled on Thursday that the latest indictment would go ahead, despite a defence argument that "new evidence" was full of shortcomings and should be thrown out.
"There is no reason for the court to declare that the charges were incomplete," chief judge Sudarto said, delivering the decision of the five-judge south Jakarta court panel hearing the case.
The decision, given in Bashir's presence, is likely to be welcomed by such countries as the United States and Australia that connect him to the Bali nightclub bombings in 2002 and the JW Marriott hotel attack in 2003.
Sudarto said that the court would start hearing witnesses in the next session.
Bashir was arrested shortly after bombs ripped through two nightclubs in Bali, killing 202 people, but courts later ruled charges brought under the criminal code over his leadership of the al-Qaida-linked Jemaah Islamiya group, and his links to earlier violence were unproven.
He served 18 months for immigration violations instead but was re-arrested in April at the end of that sentence with police using anti-terrorism statutes rather than the criminal code in their investigation of the case.
Bashir denies involvement in terrorism and says the charges result from Western pressure on Indonesia's government.
The Jemaah Islamiya network has also been blamed for a 9 September bombing outside the Australian embassy in Jakarta which killed 10, as well as planned and actual attacks in other Southeast Asian countries.