Earlier this year, a Thai court ruled that soldiers killed six protesters during the crackdown.
Suthep was in charge of the ad hoc government-run security agency set up to contain the protests.
The pair, both opposition Democrat Party lawmakers, are currently shielded from trial by parliamentary immunity while parliament is in session, but can be formally indicted once the session ends Nov. 28.
Democrat Party Spokesman Chavanond Intarakomalyasut said Monday that the two are willing to fight the accusations in court.
The indictment decision, made by Attorney General Atthapon Yaisawang, marks the first prosecutions of officials for their roles in the 2010 political violence. Earlier this month, the Attorney General's Office decided not to indict Thaksin on terrorism charges even though other Red Shirt leaders were prosecuted.
But any charges against both sides of the political divide might be voided if the parliament passes a contentious draft bill to grant a blanket amnesty to those involved with political conflict since the 2006 coup.
The draft, preliminarily approved by a House committee, has been criticized, with opponents saying it could whitewash Thaksin's cases and pave the way for his return to Thailand. He has been in self-imposed exile to avoid serving a two-year jail term for a 2008 conflict of interest conviction.
It would also give immunity to Abhisit and Suthep for any involvement in the 2010 crackdown.