If found guilty on the charge of negligence, Yingluck Shinawatra could be jailed for up to 10 years.
The anti-corruption agency has also called for Yingluck Shinawatra to be personally liable for losses to state coffers.
Yingluck Shinawatra 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.
Yingluck Shinawatra was not at Bangkok’s Supreme Court to hear the indictment.
Under the rice subsidy scheme Yingluck Shinawatra’s Pheu Thai-led government bought rice from Thai farmers at above the market rate, costing the government billions of dollars.
Critics accused Yingluck Shinawatra of funneling 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 March 19 whether to pursue the criminal case.
Additionally, Finance Minister Sommai Phasee said on February 18 that the ministry had received a letter from the national corruption watchdog urging it to pursue civil suit against Yingluck Shinawatra to recover losses of 600 billion baht ($18.4 billion) 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 Yingluck Shinawatra’s government.
Thailand has been embroiled in a cycle of political instability since the military ousted Yingluck Shinawatra’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 Shinawatra-linked parties, under various different names, have won every election since 2001.
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