Powers to enable workplace parking levies to go ahead are due to come into effect next month, with Edinburgh and Glasgow city councils among those interested in introducing schemes.
Income would be ring fenced for transport improvements.
It follows Nottingham becoming the first council in the UK to introduce a scheme in 2012, which Ms Gilruth said had raised £56 million in its first six years.
Scottish Conservatives transport spokesperson Graham Simpson told the Scottish Parliament’s net zero, energy and transport committee he was “astonished” at the lack of any limit to the charge, which is £428-a-year per space in Nottingham.
He said: “That will frighten the life out of businesses across Scotland.
"The Scottish Chambers of Commerce and Glasgow Chamber of Commerce are saying this levy should be scrapped or at least put on hold while we recover from the pandemic.”
However, Ms Gilruth said: “This is a matter for local authorities to decide upon.
"If I was to come and set a top limit for this, I would be accused of interfering with local democratic principles.
"We’ve got to get the balance right here.
"I think it’s really important that local authorities are trusted to look at their local circumstances.
"I would expect them to set an appropriate cost accordingly.
"I would be concerned that Mr Simpson is potentially scaremongering on this issue."
But Mr Simpson said: “I’m not scaremongering.
"I was asking about the charge for the licence and there isn’t, as you’ve confirmed, an upper limit for that.”
Committee convener Dean Lockhart pointed out councils were limited as to how much they could raise council tax levels.
The Scottish Conservative MSP said the lack of a limit could potentially cause “some concern for businesses, large and small throughout the country who might have to pay it”.
Ms Gilruth said she would write to the committee with the rationale for not imposing a limit, as she was not the minister when the legislation was introduced.
However, she said: “We don’t want to make this a prohibitive measure at all.”
The scheme would not cover shopping centres or retail parks, but councils could choose to include schools, colleges and universities.
Other exemptions include healthcare workers at hospitals.
Scottish Liberal Democrat transport spokesperson Jill Reilly described the lack of a limit as “dire news for ordinary Scots already facing a cost-of-living crisis".
She said there had been little thought of the impact on those in urban areas “whose streets will be blocked with displaced vehicles, and those who can’t get public transport to their work”.
The Scottish Retail Consortium has called for the plans to be paused or safeguards added such as a cap on the levy “so it is not punitive”.
Director David Lonsdale said: “Such levies remain a recipe for extra cost and complexity, especially as firms already pay business rates on the parking places they provide for staff.”