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.
"It's a big fire, it's in the public interest and we don't want to be left wanting."
A fire investigator arrived later on Monday and spent about an hour and a half inspecting the building in an effort to ascertain what started the fire.
The Thain's building is a class B heritage building in the Whanganui District Council plan, but it has no national heritage status.
Eleven fire crews from as far away as Palmerston North and New Plymouth rushed to it on Saturday night after multiple calls came in about it being on fire at 8.45pm.
Of the two men injured, one 46-year-old has been discharged from Whanganui Hospital and another remains there in a stable condition.
Craig said 12 police officers remained at the scene of the fire until it was extinguished at 12.55am.
"Our involvement is always keeping the peace and ensuring people's safety. Staff assisted with evacuations and scene control," he said.
"There were a lot of people there, we made sure nobody broke through the cordons and we helped evacuate a number of people from the building."
Detective senior sergeant Neil Forlong is leading the police investigation and said they will have a cleaer view of what is happening on Tuesday.