Mohamed Amin Razali is the group's leader
The men could be sentenced to hang, or receive life prison sentences.
The final sentences are expected on Friday.
The leader of the Al-Ma'unah group, Mohamed Amin Razali, and his followers were captured after a jungle shoot-out 18 months ago in northern Perak state.
They had stolen a large number of weapons, and held hostages for several days, two of which were killed by the group prior to their capture.
The judge, Zulkekli Ahmad Makinudin, said the other accused had pointed to Mohamed Amin Razali as "responsible in waging a war to topple the government in the name of jihad".
Mohamed Amin Razali appeared in the court handcuffed to two policemen and never spoke during the 15-month trial.
Mystical powers
The defendants were charged with waging war against the king, the country's constitutional head of state.
Six members were sentenced to 10 years' imprisonment last December, on the lesser charge of making preparations to wage war.
In July last year, the al Ma'unah members posed as army officers and removed more than 100 rifles and large quantities of ammunition from two bases.
Attorney General Mohtar Abdullah alleged that al Ma'unah members had also been involved in other violent incidents.
These included an attempted attack on a power installation in Perak, and grenade attacks on a brewery in Kuala Lumpur and a Hindu temple at the Batu Caves - a popular tourist destination just outside the city.
Mohamed Amin Razali and his followers believed mystical powers protected them from harm.
Two-thirds of Malaysia's 23 million people are Muslim, and such cases of religious extremism are rare in the country.
Al Ma'unah described itself as a self-defence army for suppressed Muslims.