Ms Yingluck was accused of allowing the rice programme to continue despite advice it was potentially wasteful and prone to corruption.
The government has lost billions of dollars on the subsidy plan, which also cost Thailand its position as the world's leading rice exporter as the government stockpiled the commodity.
National Anti-Corruption Commission chief Panthep Klanarongran said the agency voted unanimously that there were enough grounds to indict her.
Commissioner Vicha Mahakun said: "The NACC had submitted letters to warn the defendant twice that the project would create problems and incur great losses, as well as allow corruption to take place throughout every step of the scheme.
"Yet the defendant did not consider suspending the project as soon as she learned about the country's great losses from running the project."
Ms Yingluck now faces an impeachment vote by the senate. If impeached and found guilty, she would be barred from politics for five years.
The anti-corruption commission, one of several independent state agencies with powers similar to those of a court, is also looking into possibly filing criminal charges against Ms Yingluck.
The decision came a day after the Constitutional Court ousted Ms Yingluck and nine cabinet members for abuse of power over the transfer of the National Security Council chief in 2011 to another position.