"He is facing serious charges [for actions] which led to a crisis of confidence in Thailand," Sirisak Tiyapan, from Thailand's attorney-general's office, said.
"Everything will be done according to the law, but we already consider it a success that he was sent back to face justice."
Saxena appeared in court in a wheelchair, saying he needed medical treatment because of a stroke he suffered in March.
The court remanded him in custody for 12 days on the condition that he was kept in the jail hospital.
Bank collapse
Saxena is accused of embezzling $88 million from the Bangkok Bank of Commerce, which collapsed in 1995, helping trigger the 1997 Asian financial crisis.
He was a financial adviser to the bank, which made millions of dollars of fraudulent loans to cronies of the management.
Saxena fled to Vancouver and was arrested in July 1996 at the request of Thai police.
He lost his 13-year fight against extradition when Canada's supreme court refused to hear his case on Thursday. Within hours, he was transferred to Thai authorities.
Saxena denies all the allegations against him.
"He fully co-operated with police but he denied all allegations, so this morning police brought him to Bangkok southern criminal court to seek court approval for his first remand," police said.
Government 'serious'
The case is still pertinent because those who received the fraudulent loans, include several still-prominent politicians.
Abhisit Vejjajiva, the Thai prime minister, whose party first revealed the scandal at the bank during a parliamentary debate, called for the legal process to proceed unhindered.
"(The government) is serious about this case ... there will be no protection for those involved," Vejjajiva said.
"If anyone is implicated, they will have to answer to the charges."