Yoon's critics have said his desire to move the office was tied to his belief in feng shui, a traditional religious practice which stresses the importance of harmony between humans and nature.
The former prosecutor has been dogged by accusations of ties to a shaman, which he has denied.
The Blue House has long been rumoured to foster bad luck for its residents, given the assassination, impeachment, corruption trials and imprisonment that have befallen South Korean presidents.
Yoon's vow that he would not spend a single day in the Blue House compound even drew criticism from his predecessor Moon Jae-in, who called the decision "dangerous" amid heightened tensions with North Korea.
"It is hard to understand how the decision was formulated to determine Yoon would not spend a day at the Blue House," Moon said last month.
The move is also to blame for Yoon's record-low approval rating of just 41 percent, according to a recent Gallup poll.
Yoon started his term in office with a security briefing in an underground bunker, as he faces an increasingly belligerent Pyongyang.
North Korea has conducted a record 15 weapons tests since January, including two launches just days before his inauguration.
