The Seoul Western District Prosecutors' Office said it requested the warrant on charges of sexual intercourse and sexual harassment by abuse of occupational authority, citing the risk of him destroying evidence as he has denied the charges.
If convicted, he could face up to five years in prison or a 15 million won ($13,000) fine.
The 54-year-old is accused of sexually assaulting his former secretary and another female researcher from a think tank multiple times over the past year.
But the charges that have been made for the warrant only include the ones for the case involving the secretary. An investigation is still underway for the latter victim, prosecutors added.
The secretary, Kim Ji-eun, made the revelation in a TV news interview early this month and filed a complaint with the prosecution.
An, once a prominent liberal politician who was considered a potential presidential candidate, resigned as governor over the scandal.
He has undergone questioning by prosecutors twice. He apparently denied the charges, saying the sexual relations were consensual. (Yonhap)