He believed most of those houses would be found to be perfectly safe.
He had asked officials for advice on whether the current standard or threshold for contamination was set at the right level. A new standard could be set within months.
"The fact is, the police will tell you that people aren't manufacturing P in houses anymore. They are in clandestine labs in the bush in a remote location."
Twyford referenced the case of Robert Erueti, who was evicted from his state house where he lived for more than 15 years, after traces of meth were detected.
"A very, very tiny amount of methamphetamine residue was found on his property. I don't think there was any suggestion that he was responsible for that," Twyford said.
"He was evicted from his property and spent the last 14 months living in a grotty boarding house and then homeless. It is a mad policy, it is unfair."
Asked if such cases could result in compensation, Twyford said he wasn't ruling anything in or out.
National's housing spokesman Michael Woodhouse said his predecessor was already working on a new standard.
"I haven't seen exactly what Mr Twyford has said about that, but it would be nothing new. I think we realised that the thresholds for meth testing was set a little high and we needed to come to a sensible arrangement.
"It is ultimately up to the public policy makers to set the thresholds and we certainly identified an issue as the previous Government that was being worked on."
Standards NZ released a new meth testing standard this year, raising the maximum acceptable level of meth contamination to 1.5mcg per 100cm2.
The NZ Drug Foundation has called the industry that has grown around meth testing and clean-up "the biggest scam this country has ever seen".