In the Budget, Treasury had halved its forecasts of the additional investment associated with KiwiBuild from $5.4 billion to $2.5 billion by 2023, saying while the full investment activity was not lost, it believed it would take longer.
Ardern said in defence of Twyford that MBIE had very different predictions and it was not unusual for Government departments to have competing views.
Twyford's comments prompted a rebuke from the Public Services' Association, which said ministers should not personalise criticism of public servants.
It is not the first time Twyford has questioned officials' KiwiBuild projections.
In March he rejected MBIE's assessment that a household would need an income of $113,000 a year to afford one of the $600,000 homes in the programme.
The former National Government also sometimes took Treasury to task.
Former Minister Gerry Brownlee was a regular critic of Treasury's earthquake-related forecasts, describing them on separate occasions as "rubbish," done by people who "fluff about the place pontificating", and "utter tripe".
Labour's Megan Woods had described Brownlee as "a bit like a 12-year-old stamping his feet and telling his parents it's the teachers fault for a bad report."