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 December 3 martial-law declaration amounted to insurrection.
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 Suk-yeol has failed to respond to summons for questioning over his martial-law declaration. (AP PHOTO)
Yoon Kab-keun, a lawyer for the suspended president, said the arrest request was "unfair" and the anti-corruption agency had no authority to do so.
"Emergency martial law is within the president's authority," the lawyer told reporters on Monday outside the Seoul Western District Court after submitting a written opinion about the arrest warrant request as well as a letter of appointment of lawyers.
Yoon was suspended from presidential powers after being impeached by parliament over his decision to briefly impose martial law.
Masked martial law troops equipped with rifles, body armour and night-vision equipment entered the parliament where they faced off with staffers who opposed them with fire extinguishers.
The decree lasted just hours until the parliament voted it down and Yoon backed down.
The move shocked the nation, which has been a democracy since the 1980s, caused international alarm among allies such as the United States and trading partner's with Asia's 4th largest economy.
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.
On Friday, the court held its first preparatory hearing where a request by Yoon's lawyers for a postponement in proceedings to better prepare was denied.
The court said it would move swiftly.
The next hearing is due on January 3.
