The Jatiya Party MP from Nilphamari has 50 days to deposit the money to Bangladesh Commerce Bank if he wants to uphold the bail which was granted by the trial court.
The court's order came on Sunday after disposing of a previous rule over the MP's bail in the cases filed by the Anti-Corruption Commission or ACC.
Chowdhury stands accused of amassing over Tk 942 million taken in loans from the Bangladesh Commerce Bank.
In May 2016, the ACC filed two cases with Dhaka's Bangshal police against Chowdhury and eight others.
Commerce Bank counsel Sarwar Hossain claimed Chowdhury now owes the bank Tk 1.34 billion, including interest for the loans.
In August last year, Chowdhury secured a four-week anticipatory bail from the High Court. He later surrendered to the trial court and was granted mail.
In November 2016, suspects Asaduzzaman and Gani sought bail from the High Court, when the court issued a rule asking why Chowdhury's bail granted by the trial court will not be cancelled.
On Sunday, Justice M Enayetur Rahim and Justice Shahidul Karim of the High Court disposed of the rule and said the lawmaker has to pay the bank to keep his bail.