Under the subsidy scheme, a flagship policy of Ms Yingluck’s administration, the state paid farmers way above market prices for their rice.
Ms Yingluck now faces a ban from politics after a senate hearing.
“The committee has investigated and there is enough evidence to make a case,” the National Anti-Corruption Commission president, Panthep Klanarongran, said.
If found guilty by the senate, Ms Yingluck could be banned from politics for five years.
“The scheme incurred huge losses and had weaknesses and risks at every level from the registration of farmers to the sale of the rice,” Commissioner Vicha Mahakun told reporters.
The decision comes a day after the Constitutional Court removed Ms Yingluck from office for abuse of power.
Commerce Minister Niwatthamrong Boonsongphaisan will step into the prime minister’s role and says the caretaker government will press ahead with plans for a July 20 election.
Activists from both the pro and anti-government sides are planning big rallies in Bangkok in the coming days, raising fears of clashes.
Twenty-five people have been killed since the protests began in November. [Australian Broadcasting Corporation]