More than 120,000 Windows-based computers running Internet Explorer 9 are infected in the U.S., researchers say.
The click-fraud auditor says it built software in partnership with Yahoo that lets advertisers automatically deal with the costs of fraudulent clicks in a search ad campaign.
Microsoft has launched a stinging attack on Google over accusations that Bing copies Google's search results.
The software maker accuses science news aggregator RedOrbit of engaging in a scheme to get paid for fraudulent clicks, but the site's operators deny accusations.
As part of a class-action settlement, Yahoo plans to create a new ad distribution option that will give advertisers more control over where ads purchased through Yahoo appear.
The industry-first partnership gives Yahoo a way to distinguish itself from Google.
Click Forensics concludes that bogus clicks on online advertisements rose to 17.1 percent for the fourth quarter, driven increasingly by botnets.
Bogus clicks on ads, which can make money for Web sites but cost advertisers, were no more common in the second quarter. But click fraud is getting more sophisticated.
A plaintiff-only firm that has successfully gone after Yahoo and Google in the past says Citysearch is "encouraging" click fraud.