"These earthquakes are very, very common and many of them would go unnoticed," he said. "It is possibly unfortunate that the two largest events just happened to be in sequence."
Mr Scott said the village suffered little damage but there had been anecdotal reports of hot water springs appearing in new places, streams drying up and a waterfall at Waihi's northern end shifting several metres.
John Mariu, who lives at the village's northern end, said Monday's evacuation was the first he could recall in more than 50 years living there.
He left his wooden cottage with little more than a change of clothes and headed to a relative's house in nearby Tokaanu certain he would be back at his home later this week.
Yesterday morning he was allowed to return briefly to feed his cats as others collected some belongings or prayed in the church.
"The deadline for us to go back to the village is on Friday," Mr Mariu said. "You can guarantee that I am going back to my home then."
Another Waihi local, who did not want to be named, was woken by a "booming" sound on Saturday morning before her house shook. She sought shelter under her bedroom door frame.
"You are always expecting another jolt and just when you get back to sleep, well hello, there's another big one.
"We had a few more after that so it didn't take much to convince me to get out when the Civil Defence guys came around."
Taupo District Council communications manager Suzanne Takiwa said a team of geotechnical experts and seismologists were collating information on the area.
She said the council was awaiting their feedback and it was unlikely people would be able to return to their homes before Friday. State Highway 41 between Tokaanu and Pukawa is also likely to remain closed until Friday.