Yoon has failed to respond to summons for questioning by police and the Corruption Investigation Office for High-ranking Officials who are jointly investigating whether his Dec. 3 martial-law declaration amounted to insurrection, Reuters reported.
Police have tried but failed to successfully raid the presidential office as part of the investigation.
A Seoul court will decide whether to issue an arrest warrant following the request.
Insurrection is one of the few charges for which a South Korean president does not have immunity.
Yoon Kab-keun, a lawyer for the suspended president, said the arrest request was "unfair" and the anti-corruption agency has no authority to do so.
Yoon was suspended from presidential powers after being impeached by parliament over his decision to briefly impose martial law.
The decree lasted just hours until the parliament voted it down and Yoon backed down.
A Constitutional Court trial has commenced into whether to reinstate Yoon or remove him permanently from office. It has 180 days to reach a decision.