The couple allegedly benefited from an illegal real estate deal in 2003.
Pojaman, who returned to Thailand early this month saying she wants to prove her innocence in court, is accused of using her husband's political influence to buy prime Bangkok real estate at a knockdown price but has denied any wrongdoing.
She could be jailed for up to 20 years if found guilty.
But Noppodon Pattama, the couple's family lawyer, said the charges were politically motivated by "those who are trying to discredit Pojaman and her family".
Thaksin and his wife also face arrest for allegedly concealing Thaksin's ownership of millions of dollars worth of shares in the country's stock exchange.
Al Jazeera's Selina Downes, reporting from Bangkok, said critics believed that Pojaman's return had an ulterior motive – to check the political climate before her husband's return.
Thaksin's allies have managed to get back
in power under the People Power party [AFP]
Pichai Chuensuksawadi, editor-in-chief of the Bangkok Post, said he was not surprised that she had returned to Thailand.
"She's here to test the waters, to work out some sort of compromise deal for her and her husband."
Thaksin was removed from office in a military coup 16 months ago and was banned from politics along with more than 100 senior officials of his now dissolved Thai Rak Thai party for five years.
But Thaksin's political fortunes were recently revived.
His allies regrouped under the banner of the People Power party and went on to win the most number of seats in last month's parliamentary election, putting them firmly back in charge through a coalition government formed with five smaller parties.