Nothing else was taken – the Herald understands that the office wasn't ransacked at all and it appeared that no drawers had been rifled through.
Police are looking into the theft.
In a statement, a National Party spokesman implied that the theft could have been politically motivated.
"The nature of the burglary is also highly suspicious, given that our internal party offices aren't overly visible from the street, the nature of the items stolen, and that the building itself contained other items of high monetary value," he said.
He added that the party takes the security of its staff and information incredibly seriously.
The laptops in question, he said, were "very well encrypted" in "about three different ways".
The spokesman wouldn't say what information was on the laptops, but confirmed they were "normal service laptops" used by staff.
"At this time, we will let the police do their job and won't be making any further comment till the matter is investigated fully."
The Epsom HQ is also used by National MPs Paul Goldsmith and Jian Yang – none of the laptops were used by either MPs.
Goldsmith said he was worried about the possibility that the theft was politically motivated.
"There are other things they could have taken, but they only took three laptops. It is certainly a worry that it might be politically motivated.
"I hope it's not a signal of things to come."
A staff member, who did not want to be named, told the Herald this morning the break-in was "pretty odd".
He said the office was "a bit of a bunker" and was partially underground.
"You would have to know that we were here."
He said that someone had jimmied a window open during the break-in.
Asked if there was any evidence that this was a politically motivated break-in, the staff member said: "It's pretty odd; we're in a pretty quiet part of Epsom".