The First Minister said he was “extremely concerned” about the implications for those using the Holyrood building, including MSPs, staff and journalists.
His comments came after MSP Colin Smyth denied allegations he had placed a secret camera in toilets in the building.
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The South Scotland MSP was arrested on August 5 and charged with a separate offence of possession of indecent images, prompting his suspension from Scottish Labour.
His Holyrood pass was deactivated on Thursday, effectively preventing him from accessing the building.
With MSPs due to return to Parliament after the summer recess on Tuesday, the First Minister was pressed over whether the building is a “safe place to work”.
Swinney said that as the case against Smyth was live there were “strict limits” on what he could say.
He said: “I’m absolutely horrified by what has been the subject of revelations over the course of the last few weeks.
“I’m extremely concerned about what the implications for members of parliament, members of staff, journalists, for everyone who uses the parliamentary building.”
On Friday it was confirmed Police Scotland had carried out a search of toilets and changing facilities in the Parliament building, with “no covert recording devices” found.
Those using the building were also told there will be “enhanced additional checks” going forward.
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Smyth, meanwhile, issued a statement in which he rejected the allegations against him.
The MSP said: “This allegation has come as an utter shock and one I strongly refute.”
He added that “for legal reasons I can’t respond to specific matters or speculation” but stressed he was “fully co-operating” with the authorities, saying he hoped investigations could be “concluded quickly and fairly”.
The National reported how MSPs said they feel “violated” in the wake of the allegations around Smyth.
Higher Education Minister Graeme Dey said his colleagues felt “stunned” by the reports in the media around the secret camera allegations.
Meanwhile, Scottish Greens MSP Ross Greer – who was announced as one of the party’s new co-leaders on Friday, alongside Gillian Mackay – said he felt “violated” by the allegations.
He said: “I feel sick to my stomach. I know that every other user of the building – MSPs, staff, visitors, journalists – feels the same way.”
