In an interview with the BBC, Pansak Vinyaratn was asked if the programme had been a mistake.
"No, not a mistake," he said. "You can say this, though: it's not a very efficient way of spending tax money to create income."
Mr Pansak was a key architect of the "Thaksinomics" populist policies that won Ms Yingluck's brother Thaksin widespread support from 2001-06. He has been advising the current premier since 2012.
The former journalist and London School of Economics graduate also raised eyebrows last week when he said that the government's heavily hyped high-speed train projects may need rethinking.
Mr Pansak said "medium-speed" trains running on wider-gauge tracks would be more suitable and also could serve as part of a transport link between China and Europe.
The government plans to revise the pledging scheme after admitting to a 136-billion-baht loss in the first year of the programme.
The Finance Ministry has forecast losses from pledging during the next harvest year in a range of 70-100 billion baht.
The scheme, which involves purchasing paddy at 15,000 baht a tonne, 40% above market prices, has been heavily criticised by economists who say mounting losses could damage the country's finances in the long run.
The government has already spent 657 billion baht on the scheme's first two years alone, 337 billion of which was for the 2011-12 harvest year and the rest for the 2012-13 harvest. The 2013 second crop runs through September.
The 657 billion baht exceeds the 500-billion-baht revolving budget, 410 billion of which is money borrowed from the Bank for Agriculture and Cooperatives.
Rice pledging was one of the centrepieces of the Pheu Thai election campaign in 2011. Party strategists said that putting more money into the pockets of farmers would end up stimulating consumption and the economy overall.
Critics have said that a lot of the money never gets into the intended pockets but is lost to corruption and inefficiency.
Even millers who are being paid to store huge stockpiles of rice have grown unhappy, according to the BBC.
"For the past 30 or 40 years our business grew very well under the free market system, buying and selling rice," miller Pramote Vanichanont told BBC correspondent Jonathan Head.
"But since the new rice scheme started, we've become just like government employees."