Christmas 2000 attacks
Police said Mr Ba'asyir plotted to assassinate Indonesian President Megawati Sukarnoputri while she was deputy leader, and masterminded a spate of bomb attacks on churches across the archipelago on Christmas Eve 2000.
National police spokesman Edward Aritonang said police gave the prosecutor's office evidence files on Mr Ba'asyir on Monday for consideration.
Under Indonesian law, if prosecutors believe there is enough evidence to substantiate the charge, a trial date will be set.
The recommended charges carry a maximum sentence of life for treason and 15 years in prison for attacks using explosives.
Indonesian legal system
Mr Ba'asyir has not been formally accused of taking part in last year's terrorist attacks on Bali, in which nearly 190 people were killed.
Militant network
But he is believed to be one of the leaders of Jemaah Islamiah, an Islamic militant group which is suspected of involvement in the bombings.
Several of the suspects arrested in connection with the Bali attacks are also said to have studied under Mr Ba'asyir.
The elderly cleric was arrested on 20 October, amid angry protests from his supporters.
He is accused of overseeing the delivery of bombs to 38 churches or priests across Indonesia on Christmas Eve 2000. Nineteen people were killed in the attacks.
If his trial goes ahead, witnesses in Malaysia and Singapore will give evidence via a televised link, police said last week.
Mr Ba'asyir has denied any involvement in terrorist acts and has also denied being a member of Jemaah Islamiah.