He was responding to comments by an academic at the National Institute of Development Administration (NIDA) that he and his colleagues plan to submit an open letter to Prime Minister Yingluck Shinwatra, asking her to scrap the scheme.
Mr Boonsong said continuing the scheme was not a violation of the charter and the government is not running a rice trading business, as alleged.
The minister said he expected at least 25 million tonnes of rice would be mortgaged by farmers under this scheme by next year.
Adis Issarangkul Na Ayutthaya, dean of the School of Development Economics at NIDA, earlier said that academics at NIDA would jointly submit an open-letter to the prime minister demanding the government put an end to the rice price pledging scheme.
Mr Adis said the government had incurred heavy losses running the scheme and they would launch a campaign to collect signatures of academics in support of their petition.
If there is no response from the prime minister he and his colleagues will consider future action, which might include filing complaints with the Constitution Court or the Administrative Court asking that they order the government to end the price pledging scheme.
The prime minister echoed the comments of the commerce minister, insisting on Thursday afternoon that the government would certainly continue with the rice price pledging scheme, which was aimed at raising farm incomes.
Asked about criticism the government had more or less set up a rice firm to compete with private rice traders and that this was a violation of the constitution, Ms Yingluck said it was not true.
She said the government had no intention to compete with the private sector, or to look for any profit from the scheme, but just to help farmers by enabling them to get a higher price for their rice harvest.
Ms Yingluck said the government will take into account all suggestions and expressions of concern by various parties and improve the rice scheme to ensure transparency in the pledging process.
The government was ready to hold talks with the private sector, to listen to its problems and help find solutions, she added.
The prime minister said farmers deserved sympathy, and the pledging prices set for rice were the highest in the general region.
Private firms can buy rice directly from farmers if they want to, she said.
Deputy Prime Minister Chalerm Yubamrung also gruffly brushed aside the academics' criticism of the rice price pledging scheme as a violation of the charter - which does not allow the state to compete with private enterprise - and financing the pledging scheme as too expensive.
Mr Chalerm said on Thursday the academics were acting like an opposition outside parliament, and their criticism was worthless and lacked credibility.