A Tokyo district court spokesman said Mr Asahara and his aides had been charged with releasing sarin nerve gas on 20 March, leaving 12 dead and 5,500 injured, and terrifying the Japanese public.
Nine other members were charged with conspiracy to murder. According to police, the 40-year-old guru sat in his cell at the Tokyo police headquarters throughout the formal charging.
Detention warrants for Mr Asahara and other key suspects expired yesterday and prosecutors had either to charge or release them. Seven other cult members wanted for murder are still on the run.
The charges are considered a crucial step in easing the fears that have gripped the public since the subway attack. But the Prime Minister, Tomiichi Murayama, still ordered police to pursue the investigation. "Many questions remain unsolved," Mr Murayama said. "I want the police to make a continued effort in resolving the case and removing public unease."
Hiromu Nonaga, the Home Affairs Minister, said police were convinced that cult members had no more sarin in reserve.
The trial cannot start until the investigation, expected to last at least until August, is completed. "We don't think we have resolved 100 per cent of the case, but we are 100 per cent confident that Asahara will be found guilty of murder," a senior prosecution official said.
Mr Asahara, whose real name is Chizuo Matsumoto, was detained on 16 May at the cult's commune at Kamikuishiki, at the foot of Mount Fuji. He at first insisted he was innocent but has since refused to answer questions about the attacks and other allegations.
However, police reportedly have confessions from his associates that the sect produced the sarin and used it in the Tokyo trains under Mr Asahara's instructions.