PageFair provides analytics that allow publishers who sell inventory through ad networks to detect when readers are using ad blockers, and substitute “non-intrusive” ads for the blocked ads to reclaim some of the lost revenue.

Hackers apparently used PageFair’s own analytics network to distribute Trojan malware during a 83-minute period; the attack was detected within five minutes but took over an hour to stop.

A small proportion of PageFair’s customers (2.3%) were affected, and even within this small number, relatively few visitors would have actually been infected, but PageFair CEO Sean Blanchfield didn’t try to minimize the security breach.

He noted: “If you are a publisher using our free analytics service, you have good reason to be very angry and disappointed with us right now… I am very sorry that this occurred and would like to assure you that it is no longer happening… The attack was sophisticated and specifically targeted against PageFair, but it is unacceptable that the hackers could gain access to any of our systems.”

The Javascript Trojan, disguised as an update to Adobe Flash, infected computers using Windows to get them to join a botnet. Some virus scanners on were able to detect the malware and prevent infection, but not all. On a positive note, PageFair said none of its core servers appear to have been breached, so publishers’ accounts should be secure.

Of course, ad blocking itself is still a growing threat to publishers’ business. This week, a Dutch tech site, Guru3D.com, said ad blockers were costing it roughly half of its ad revenues in a blog post urging readers to turn off ad blocking programs, according to Bloomberg.