The government has ordered Deputy Prime Minister Kobsak Sapavasu to sort out the mess.
He estimates it has already cost 11 billion baht ($325m) just to process and store crops bought under the mortgage scheme.
And because rice prices have fallen this year, when the government sells the stocks he estimates it will lose another 20 billion baht ($590m).
“The numbers are just unbelievable,” says Mr Kobsak.
But his attempts to close down the mortgage scheme, and replace it with a simpler subsidy, have been blocked by his own coalition partners.