Questions had been raised as to why the car parks had remained open when the city council closed all of its car parks beside parks.
The Scottish Government agency said all car parks in Holyrood Park except one would close from tomorrow.
It said the decision followed needless travel by people driving to the park.
The car parks at Duddingston and Meadowbank triangle by St Margaret’s Loch will be closed.
Only Broad Pavement car park, east of the Palace of Holyroodhouse, will remain open.
There have also been calls from walkers and cyclists to re-impose the normal Sunday traffic ban through the park to provide more space for exercise.
Stuart Hay, director of Living Streets Scotland, which campaigns for walkers, said: “We are delighted Historic Environment Scotland finally have seen sense and stopped encouraging people to drive in their park during the pandemic.
“They need to go further by closing the main roads to traffic, which is coming into conflict with walkers and cyclists who are trying to keep a safe social distance.
“With the car parks closed, these roads serve little function and would better serve as pleasant space for cycling and walking.”
A spokesperson for the agency said: “Due to an increase in usage of the car parks at Holyrood Park, and some members of the public not following [Scottish] Government guidance and travelling unnecessarily, we have taken the decision to close the car parks, except for Broad Pavement car park, as of Friday 1 May.
“Broad Pavement car park will remain open to enable those with mobility issues to enjoy the park, and to allow key staff at the Scottish Parliament to use the car park, as well as other key workers in the area.
“We have contacted local residents who will be affected by the closures, and we are working with Police Scotland who will monitor usage of the car parks and enforce where necessary.”
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