The SNP leader 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.
The South Scotland MSP was arrested on Tuesday 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”.
Mr Swinney said to the PA news agency that as the case against Mr 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.”
As such, he said it was “so important that parliamentary authorities provide that clear and definitive reassurance to everybody involved”.
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.
MSPs will return to business at the Scottish Parliament on Tuesday (Jane Barlow/PA)
Those using the building were also told there will be “enhanced additional checks” going forward.
Mr 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”.
Speaking at Glasgow Caledonian University on Monday, Scottish Labour leader Anas Sarwar said: “It’s deeply distressing and shocking for all of us and for people across the parliamentary estate, no doubt.
“As soon as we became aware of the seriousness of the allegations, Colin Smyth was suspended. He now sits as an independent MSP.
“This is, of course, an ongoing investigation, it would be inappropriate for me to comment further on any questions about the Parliament.”