Mr Niwattumrong said a Chinese state company terminated a contract to buy 1.2 million tonnes of rice.
He said the company was afraid it would run into problems due to an investigation by the National Anti-Corruption Commission (NACC).
The rice scheme is a flagship policy of Prime Minister Yingluck Shinawatra's embattled caretaker government.
Critics say the policy of buying rice from growers at above market prices has accumulated losses of at least $4.46 billion and has been dogged by corruption.
Thousands of farmers have blocked main roads in the provinces to demand overdue payments from the government.