The chargesheet was filed before the chief judicial magistrate here.
Augustine committed suicide last year after he felt that he would be arrested.
The CBI had arrested the remaining three Nov 19 last year but all of them secured bail Jan 1 this year.
The CBI was called in to investigate the controversial case after 12 earlier teams failed to come up with convincing leads.
The charge sheet also mentions that four others, a nun, retired superintendent of police K.T. Michael and two lady workers of the convent will have to undergo narco-analysis tests as part of the investigation.