Sections of Taupo Quay and Victoria Ave closed as firefighters extinguished a hotspot inside Thain's building more than 36 hours after a massive fire tore through it.
Wispy white smoke could be seen streaming from the roof of the Victoria Ave building on Monday morning as two Whanganui fire crews attended the scene.
Thain's building was damaged extensively by a blaze that burned through it for over four hours on Saturday night, injuring two people.
Police were also at the scene on Monday morning, which sergeant Mike Craig said would be under guard until fire investigators arrived.
"At the moment we don't know the cause of the fire," Craig said.