The road is also completely washed out and closed.
The couple's neighbour and property landowner, Chelsea Luke, said the rain had since stopped but she could see dark clouds hanging over hills in the distance.
She said the house that was flooded was directly next to a "dry wash" or a creek that is normally dry. However, because of the flash flooding, logs had been been swept down the creek causing a build-up of water which flooded the house.
More flooding in Galatea. Photo / Te Akauroa Miki
Ms Luke said she got a call at 7am today advising her that her neighbours were in trouble.
However, she was relieved to see them finally get rescued and that they were okay, although the female occupant had been checked by St John Ambulance staff.
"I was more concerned about them than me ... our [farm] worker called in and said that he could see logs that were about halfway up their house."
She said their property had been in her partner's family for decades and said this morning's deluge was the biggest they had heard of since the 1960s.
Despite floodwaters also trapping her and her daughters on their property, their driveway had since been cleared.
However, there was a large amount of debris, including large logs, and silt lying on their property. A small bridge had also been destroyed, she said.
The local council is also being called to clear about 200m of logs which are blocking the road.
Heavy machinery is being brought in to help clear the road and re-direct flood waters.
The emergency comes as severe thunderstorm watch has been issued for parts of the North Island.
MetService said Bay of Plenty, Coromandel Peninsula, Rotorua and Great Barrier Island could expect heavy rain, including thundery, localised downpours this morning.
It said the heavy rain had now eased on the South Island's west coast and has cancelled the heavy rain warning for Fiordland, Westland and Buller.
A picture taken from space shows the strengthening cyclone which has now done a u-turn and is lashing Tonga for the second time this week. Photo / NASA
But those regions could still expect some heavy showers in those regions until just after midday.
A second weak front was expected to bring brief spells of rain to western areas of the North Island.
Forecasters said a front and a band of heavy rain would move slowly over northeastern regions and on to eastern Bay of Plenty before clearing this afternoon.
These regions could expect sudden bouts of rainfall measuring between 25mm and 40mm an hour which was enough to cause flash flooding and make driving hazardous.
