"The prisoners have been able to access some parts of the building by breaching the roof space, however their movement inside the building is restricted by internal gates, barriers and secured doors.
"There is a large amount of smoke around the building which is coming from mattresses set alight by the prisoners."
While there is no threat to public safety, Corrections staff have moved 49 prisoners from one unit to elsewhere in the prison while the incident continues.
"There are around 230 prisoners in total in the 'top jail' facility and we will not hesitate to evacuate further prisoners if it becomes necessary in order to keep them safe."
FENZ were originally called to Waikeria after inmates lit several fires in the prison's exercise yard on Tuesday afternoon.
About 20 prisoners were using the yard at the time.
The situation was thought to be under control before nine prisoners refused to comply with instructions, Newshub reported.
Offenders allegedly took toilet doors off their hinges and used them as weapons against staff.
Corrections Association president Alan Whitley said the union was offering support.
"We're always concerned about people when a situation like this is going on, but we've got specialised teams that have got specialised training, they're professional people and they'll do a professional job to get the situation under control," Whitley told RNZ.
St John staff treated a number of staff and prisoners due to smoke inhalation. Earlier in the evening it was thought at least one prisoner was bleeding after an altercation with guards.
A prisoner on remand said a riot at the prison had been imminent, with prisoners protesting for basic human rights. They claimed there were issues at the prison, including toilet paper taking days to be provided, Newshub reported.
Last year, two Waikeria Prison Correction officers were punched in the face within nearly as many days, while fighting between prisoners has also been reported.
A prisoner punched an officer in the face and another officer was also injured when he stepped in to help.
That altercation came after an officer was threatened and punched a few days earlier.
There had also been reports beforehand of prisoners fighting among themselves.
Waikeria Prison is one of New Zealand's biggest prisons, located on a 1200ha site south of Te Awamutu in the Waikato region.
The 'top jail' where the inmates are currently contained was built in 1911 and is the oldest part of the prison. It is being replaced by a new facility being built at the prison and which is scheduled to open in 2022.