If found guilty on the charge of negligence, she could be jailed for up to 10 years.
The anti-corruption agency has also called for her to be personally liable for losses to state coffers.
Ms Yingluck was removed by a court in May 2014, shortly before the military ousted her elected government.
She was later impeached over the rice subsidy scheme and banned from politics for five years. Thailand, meanwhile, remains under martial law in the wake of the coup.
Ms Yingluck was not at Bangkok's Supreme Court to hear the indictment.
But the BBC's Jonathan Head in Bangkok says today's court filing will seem to her supporters like yet another attempt by the military to crush her politically for whenever Thailand does return to democratic rule.
Under the rice subsidy scheme Ms Yingluck's Pheu Thai-led government bought rice from Thai farmers at above the market rate, costing the government billions of dollars.
Critics accused Ms Yingluck of funnelling money to her core supporters. She said the policy was aimed at helping farmers and denied any day-to-day involvement in the running of the scheme.
The Supreme Court will decide on 19 March whether to pursue the criminal case.
Additionally, Finance Minister Sommai Phasee said on Wednesday that the ministry had received a letter from the national corruption watchdog urging it to pursue civil suit against Ms Yingluck to recover losses of 600bn baht ($18.4bn; Â£11.9bn) related to the scheme.
"The finance ministry oversees damages to the state and is ready to take action," he said.
The military seized power in May 2014 in what it said was a bid to restore public order after months of occasionally violent street protests against Ms Yingluck's government.
But Thailand has been embroiled in a cycle of political instability since the military ousted Ms Yingluck's brother, billionaire Thaksin Shinawatra, as prime minister in 2006.
The Shinawatra family are hugely popular among Thailand's rural population but are hated by the urban middle-class and elite who accuse them of corruption.
Thaksin-linked parties, under various different names, have won every election since 2001.
Thailand's attorney-general has filed criminal charges against former Prime Minister Yingluck Shinawatra over a controversial rice subsidy scheme.