Pojaman is accused of evading millions of dollars in taxes following the transfer of 1.4 million shares in Shin Corp, the telecommunication company her husband founded in 1997.
The Assets Examination Committee appointed by the coup leaders found last month that Pojaman and her brother, Bhanapot Damapong, had to pay back taxes of about $17 million.
Pojaman and her brother face a maximum penalty of 14 years in prison and a $12,600 fine each if convicted on two tax evasion counts, said Attapol Yaisawang, spokesman for the attorney-general's office.
The secretary, Kanchanapa Honghern, would face a maximum penalty of seven years and a $6,300 fine because she is accused of only one charge.
The committee is also investigating Thaksin's daughter, Pintongta, and son, Phantongtae.
Nopadol Patama, Pojaman's lawyer, said her brother and secretary were arraigned at the Bangkok criminal court and released after posting bail of $476,000 bail.
He said the trio planned to plead their innocence.
"We are preparing the best tax lawyers to fight this case in court," Nopadol said.
Pojaman declined to comment as she left the court.
Pojaman's case has no connection with the controversial $2.2bn sale of Shin Corp to Singapore government's investment arm Temasek Holdings early last year, a move which was criticised and cost Thaksin his post.
The deal, which placed strategic assets including communications satellites, in the hands of foreigners, was deemed tax-free because it went through the stock market where capital gains tax is not charged on share transactions.
Sukhum Nualskul, a political commentator, told Reuters: "If they are found guilty, even by the first-level court, the public will believe this family conspired to evade tax and this political harpoon will end Thaksin's political career.
"But if they are ruled not guilty, the legitimacy of the coup leaders and their graft investigators will be in jeopardy."