The warrant against the billionaire -- who fled to England last month to escape other corruption charges – was for his failure to appear in court for a hearing on a bank loan granted to the Myanmar government during his regime, the Thai News Agency reported.
The case stems from a conflict of interest and abuse of authority lawsuit against Thaksin.
The first warrant was for his failure to appear in court in a land deal case, the report said.
Thaksin and his family have denied all corruption charges.
The latest development comes in the midst of political protests against the ruling collation led by the People Power Party, which opponents say is only a proxy for Thaksin.
The political situation came to a head last week when Prime Minister Samak Sundaravej was told to resign by a court for hosting cooking shows on a commercial television while in office.
Samak's party then decided to nominate Somchai Wongsawat, a brother-in-law of Thaksin and currently the acting prime minister, to replace Samak, TNA reported.
Opposition leaders said they cannot accept Somchai because of his Thaksin ties, TNA said.
The protesters say the government is trying to bring Thaksin, deposed in a coup in 2006, back into politics, the International Herald Tribune reported. Somchai is a former judge.