Temer, the predecessor of current President Jair Bolsonaro, was Brazil's most unpopular leader ever and faced a number of corruption accusations on leaving office last year. He has repeatedly denied wrongdoing.
Temer, a center-right politician, took over as a caretaker figure after the last Workers Party president, Dilma Rousseff, was impeached and removed from office in 2016.
A spokeswoman for the Prosecutors Office in Rio de Janeiro told The Associated Press Thursday that Judge Marcelo Breitas had issued the arrest order for Temer.
Breitas is a Rio judge overseeing part of a sprawling corruption probe involving kickbacks to politicians and public officials. Since launching in March 2014, the so-called Car Wash investigation has led to the jailing of top businessmen and politicians, including ex-President Luiz Inacio Lula da Silva.
Temer lives in Sao Paulo, but his whereabouts were not immediately known.