Fire crews were at the scene removing water from the damaged properties.
MacGregor said it appeared the stormwater system was unable to cope with the deluge.
Whatawhata Rd resident Peter Cague has lived in his house since 1983. It's the first time he's had to be evacuated - and he hoped it would be the last.
His son, Scott, 35, lives in his father's ground level garage.
He said he was watching movies and playing video games with his partner when they heard the rain get so loud they couldn't hear what they were doing.
Next thing they knew, water started seeping, then pouring into the garage.
It eventually got knee deep, getting to about six inches from entering the main house.
Scott Cague reckoned it took about 15 minutes to flood his dad's garage, which he was staying in, ruining all of his belongings. He was unsure whether they would be covered by insurance.
Another resident who lived further along on Whatawhata Rd said they could see water rushing into driveways and that the damage looked a lot worse than they initially thought.
"An elderly lady who we saw on the street said she had lived here for 30 years and had never seen anything like it."
Whatawhata Rd resident Mike Auton said the flooding happened fast.
"When the thunderstorm happened, it just flooded very very quickly.
"I tried to clear the drains with my feet but just couldn't in time. I just got into action and started checking in on the neighbours and getting them out."
"The houses are quite damaged with low water, just up over the bottom of the floor.
Looks like there is a car that has been lost as well."
Another Dinsdale resident said the water was knee deep and water had flowed into several garages and houses.
Police have extended the cordon on Whatawhata Rd between Caernarvon St and Newcastle Rd and motorists are being diverted.
Some residents were unable to access their homes due to the roads being blocked off because of the flooding.
Another resident, who only wanted to be known as Robyn, said she "freaked out" when the water started rapidly rising in the heavy downpour.
However fortunately it hadn't gone inside her home, which she shared with her son, but the pair were also being evacuated by Civil Defence.
She said they would go and stay at her parents for the night.
Motorists in Flagstaff have also found themselves driving through large pools of water in River Rd and Te Huia Dr.
Jonny Powers captured dramatic footage of Te Huia Dr in Flagstaff being transformed into a river at 2pm today. He estimated the water was up to 50cm deep at its peak.
Residents on social media are also reporting flooding on Hyde Ave in Nawton.
Videos posted on social media show the water reaching as high as the cars' bonnets.
MetService shift meteorologist Tui McInnes said the rainfall for the area was not particularly significant, but the nature of thunderstorms was that they were very localised even though they could produce a lot of rain in a short period of time.
McInnnes said the thunderstorm went around the edge of Hamilton hitting the north and west.
Severe thunderstorms also hit the Hutt Valley in Wellington, northern Manawatu, Whanganui, Taranaki and Ruapehu today.
The thunderstorms would ease earlier this evening, but there could be rain and showers later as the remainder of the moisture dissipates out.
More thunderstorms were likely tomorrow and while it was harder to forecast thunderstorms too far ahead there was still some risk of heavier and more thundery showers on Tuesday too.
Meanwhile, thunderstorms and heavy rain warnings are also in place for Horowhenua, Manawatu and Rangitikei later this afternoon and similar thunderstorms throughout large parts of the country are likely again tomorrow.
MetService is warning there could be surface or flash flooding near streams, gullies and driving conditions could be extremely hazardous.
An earlier thunderstorm warning for Wellington has been lifted.
