The Ministry's Tenancy Compliance & Investigations Team was aware of the flats and confirmed an investigation was being conducted.
The team's national manager, Steve Watson, said they would inspect properties they were investigating if it was deemed necessary.
"We take breaches of residential tenancies law very seriously and landlords found to breach the law will be subject to enforcement action, and in the most serious cases can include taking a landlord to the Tenancy Tribunal."
The tribunal was able to issue binding orders which were enforceable through the Court, Watson said.
"The Residential Tenancies Act allows the tribunal to make various orders, and includes the ability to issue a "Work Order" – which requires a person to undertake specific work within a set timeframe. The tribunal can also put in place punitive measures if the work is not completed."
Whanganui mayor Hamish McDouall gave his backing to the investigation.
"Hopefully, when we have greater teeth to do something about it then we'll be using them because it's just no good with people living in substandard places and that ... potentially affects tenants' health.
"If anyone's having problems with somebody like Mr Ngapeka they can approach CLAW [Community Legal Advice Whanganui]. I used to work at CLAW and tenancy was one of our breads and butter. If there's issues I'd be really encouraging tenants to go there.
"Sadly until we get ... a new landlord's warrant of fitness or some teeth like that we can use, we are pretty powerless. I've been to the pink flats, I've known tenants in there and it seems the situation's certainly got worse in the last couple of years."
McDouall denounced what he called 'slumlords' and said there were a number of them in Whanganui.
"I've always been supportive of ... landlord's warrant of fitnesses. It [goes] two ways. I've got friends who are landlords and sometimes they've got tenants who are just shockers. It's a two way thing.
"But to not be slumlords and there are a handful of slumlords in town ... some of them are absentee landlords as well. It's not good enough, particularly [when] kids are growing up in pretty horrible situations."
The mayor said the council was limited as to what it could do to negligent landlords but he wanted the Tenancy Tribunal to be able to make quicker decisions that could be better enforced.
"We've got very little other investigative pathways that we could follow. Once the buildings been safe and assessed under the building act we go 'yep, that's that'.
"The ideal outcome is the landlord realising his responsibilities and actually putting some investment in. That's not just the Pink Flats, it's also Purnell House [another property owned by Ngapeka] and if he can't he should get out of the business."