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.

Hernandez, 24, has signed a three-year deal, which the Tigers have the option of extending for a further 12 months.
Hull's previous record transfer outlay was the £8m they paid Tottenham for midfielder Jake Livermore in June.
They also completed the signings of midfielders Mohamed Diame from West Ham and Gaston Ramirez from Southampton.
Hernandez has scored seven goals in 14 matches for Uruguay and made two appearances at the 2014 Fifa World Cup.
Tigers boss Steve Bruce said: "Abel is a fantastic signing and highlights just how far the club has come in such a short space of time.
"He is an exciting talent and, like myself, I'm sure the supporters can't wait to see him in action."
Hernandez, who scored 14 goals in 28 appearances to help Palermo win promotion to Italy's Serie A last season, arrives following the £12m sale of Shane Long to Southampton.
His signing takes Hull's summer spending beyond £30m.
Ben Arfa, a 27-year-old France international winger, has spent the past three seasons on Tyneside, having joined the Magpies from Marseille in January 2011 following a successful loan spell.
"Hatem is a superb addition to the squad, and brings a lot of attacking flair," said manager Steve Bruce.
Ben Arfa made 86 appearances for Newcastle, scoring 14 goals.
Thailand's attorney-general has filed criminal charges against former Prime Minister Yingluck Shinawatra over a controversial rice subsidy scheme.
[NEXT_CONCEPT]
Hull City have signed Uruguay striker Abel Hernandez from Palermo for a club-record £10m fee, while Hatem Ben Arfa has joined on loan from Newcastle.