The first warrant was issued by Dhaka Metropolitan magistrate Nur Nabi over a case accusing her of undermining the country's map and national flag. She failed to appear before the court even though the court had asked her repeatedly to attend today's hearing in the case.
Ms Zia, 72, is currently in London on a private tour.
The second warrant was issued by Dhaka's Fifth Special Judge's Court issued within an hour after the first one as she evaded appearance in a corruption case involving embezzlement of funds of an orphanage named after her husband and slain president Ziaur Rahman.
"The courts issued arrest warrants in two cases on the same day. It's a ploy by the government so that she can't return home," Ms Zia's counsel Sanaullah Mia told reporters.
The move came after Prime Minister Sheikh Hasina's government launched a crackdown on the Opposition, arresting leaders and supporters of Ms Zia's Bangladesh Nationalist Party (BNP).
Bangladesh may hold a general election next year, the first since polls in 2014 which Ms Zia's BNP boycotted over fears they would be rigged.