It has advised users to use other browsers like Chrome and Firefox until the issue is fixed.
The company was responding to a complaint from a Mac user who said he was being redirected to what looked like a phishing site, when he accessed the newspaper's home page on his MacBook Pro, using Safari.
This user, who prefers anonymity, reported the occurrence to iTWire on Monday; the problem was reported in detail on Monday.
He said he was then redirected to a page which loaded fully, with the domain reading mac-safetycheck.com followed by a number of letters which did not spell out any pronounceable word.
The text on this page read: "Your system is potentially infected with 3 viruses. Our security check found potential traces of 2 malware and 1 phishing/spyware.
"Estimated system damage: 28.1% – Immediate removal might be required."
The Guardian did not respond to a query sent by iTWire asking about the anomaly.
However, it did respond to the user's query.
"Thank you for reporting this issue. We are aware of a campaign that is using malicious advertisements to target Mac users, particularly those using Safari, to upgrade their Flash Player," an editorial assistant from the newspaper wrote to the user.
"We will soon be able to protect readers from these ads, but in the meantime we recommend using Chrome or Firefox as an alternative browser."