SAN JOSE — Malware warnings halted Internet users from visiting popular sites across the Internet on Monday morning, including the Mercury News, after Silicon Valley advertising company Netseer’s website was hacked. The company said its ads were not infected with any virus, and Google (GOOG) cleared the company and halted the malware warnings.

According to Twitter users, sites such as The New York Times, The Huffington Post, Los Angeles Times, Washington Post and many others were being blocked by Google’s Chrome browser with warnings about possible malware — malicious software that could infect a user’s computer — emanating from Netseer.

“Content from cm.netseer.com, a known malware distributor, has been inserted into this web page. Visiting this page now is very likely to infect your computer with malware,” a Chrome message said Monday morning when a user attempted to visit www.mercurynews.com.

Netseer, a Santa Clara-based startup founded in 2006 that helps target ads based on content offered by the website, suffered a hacking attack on its website, but said Monday that it was not actively issuing malware-infected ads.

“This morning at approximately 5:30 a.m. Pacific time, our third-party hosted corporate website (netseer.com) was hacked and infected with malware. Consequently, Google added our domain to the list of malware-affected websites. Our operations team went into all-hands-on-deck mode and we have successfully cleaned the site of the malware issue,” spokeswoman Kathleen Formidoni said.

Because the company’s corporate site and ad-serving infrastructure share the same domain, the block Google put up to keep malware placed on Netseer’s website from spreading also affected ads Netseer placed on other sites. However, “the malware was never served into the ad serving stream,” Formidoni wrote in an email.

Formidoni reported just after 10:30 a.m. Pacific time that Google had removed Netseer from its list of malware-affected websites, clearing up the problems.

Netseer was unsure Monday of the scope of the malware issues “since the overall problem does vary based on browser,” Formidoni said, but “NetSeer serves millions of ads a month and has a big global footprint.” She added that “many major publishers were impacted.”

In an email response to request for comment, a Google spokeswoman said the company did not comment on individual malware cases.

Bob Mason, chief technology officer for Digital First Media, said www.mercurynews.com and the company’s other websites are not infected with malware, but the company is taking steps to make sure any virus is blocked from its websites.

Other news sites took to Twitter to assure readers that their content does not include any malicious code.

“Hello, Chrome users. We’re aware some of you are seeing malware warnings about Guardian articles. Please ignore; no risk,” @GuardianTech, the Twitter account for The Guardian’s technology news, wrote Monday morning.

Contact Jeremy C. Owens at 408-920-5876; follow him at Twitter.com/mercbizbreak.