According to the Assets Examination Committee, the pair set up a company in the British Virgin Islands called Ample Rich as part of a scheme to avoid paying taxes on the sale.
They sold the shares of Shin Corp owned by Ample Rich to themselves at a price of one baht each before selling their controlling stake in Shin Corp to Temasek at 49 baht a share.
"They have to pay taxes like other corporations in Thailand"
Kaewsan Athipho, Assets Examination Committee
It was only discovered after the sale that they were owners of Ample Rich.
"The AEC ruled that [the children] intended to avoid taxes by selling the shares in an indirect manner," Kaewsan Athipho, an AEC member, said.
"They registered the company abroad but conducted business in the country. They have to pay taxes like other corporations in Thailand."
Pinthongta and Panthongtae have the right to appeal the ruling to a civil court.
The decision by the AEC, a panel that was established after Thaksin was deposed in a coup last September, is the latest setback for the family of the media tycoon.
This month, the AEC ordered Thaksin's children to pay another $172m in taxes and penalties over allegations that they had profited by buying Shin Corp shares at below-market prices before reselling them.
Pojaman Shinawatra, Thaksin's wife, her brother and secretary were charged in March with evading millions of dollars in taxes over a 1997 share transfer.
The sale of Shin Corp sparked widespread anti-government protests that eventually contributed to Thaksin's downfall.
Opponents were angered that Thaksin avoided taxes and sold off what many considered a strategic national asset to a foreign country.