Justice Mponda, who works for the online publication Malawi Voice, is facing two counts of false publication and criminal libel, including insulting the president.
The charges stem from a report sourced from a fake Banda Facebook account which announced she had resigned.
Police confirmed his arrest, saying they were still investigating.
The Media Institute of Southern Africa (MISA) said they were “keenly following” Mponda’s arrest.
Banda became president of this impoverished southern African nation in April, after Bingu wa Mutharika’s death.
Media in Malawi operate under strict regulations and activists have long campaigned for reforms.