The announcement was published Tuesday in the state-run Global New Light of Myanmar newspaper and other official media.
The military has said that widespread electoral fraud allegations were the driving force behind the coup on February 1, which toppled Suu Kyi's government.
But independent observers, such as the Asian Network for Free Elections, found no evidence of substantive irregularities in the polls, though they criticized some aspects.
Myanmar junta extends rule, promises elections by 2023
What impact could a prosecution have?
The action by the commission could potentially result in Suu Kyi's party being dissolved and unable to participate in a new election the military has promised will take place within two years of its takeover.
A notice from the commission, dated Monday, did not specify which laws would be used to prosecute Suu Kyi.