Lee Jung-hee, one of the minor party's leaders, stepped down after a party inquiry revealed a computer program used for internal online ballots had been changed several times and technical errors occurred during candidate selection, Yonhap News Agency reported Saturday.
The party's probe also found a large amount of votes had been cast through a single Internet Protocol address, an indication of voting irregularities
The voting irregularities created a rifted within the UPP and country's public prosecutors office is gathering data to conduct its own criminal investigation into the allegations.
As Lee resigned, she said there is a need for harmony so the UPP can overcome the incident.
"I have been able to overcome past adversities because of the help of party members," the party leader said.
Following Lee's resignation, Shim Sang-jung, Rhyu Si-min and Cho Joon-ho, who are all co-chairs of the party, also stepped down.