Deputy Agricultural Minister Warathep Rattanakorn said the government expects losses will be as much as 100 billion baht ($3.1 billion) for the harvest year that began September.
Rice, Thailand's staple grain, is one of the country's main exports. India and Vietnam surpassed Thailand as the world's top rice exporters in 2012 as the Thai government stockpiled rice to avoid even bigger losses.
Thai governments have intervened in the rice market through a variety of means since the early 1960s to help farmers, but the current scheme has its roots in the populist policies of Yingluck's brother, former prime minister Thaksin Shinawatra, who won landslide victories in two elections before he was ousted in a 2006 coup.
The scheme has been dogged by corruption and accusations the government has hidden its true cost. Previously, officials refused to reveal how much rice the government had stockpiled.
Warathep said the government has installed CCTV cameras at buying points and weighing stations, and put extra police officers at checkpoints to make sure that rice payments are made to farmers.