Up to 80 percent of Web sites flagged as malicious by anti-virus and search engine indexes are legitimate businesses, according to security experts.
Experts said while the security industry is on top of conventional spam and phishing attacks, more effort needs to be put into preventing and eliminating so-called drive-by-downloads.
The attacks allow hackers to redirect massive amounts of traffic by inserting malicious IFRAMES into legitimate Web sites. The hacks are usually invisible to Web site visitors and do not often draw attention from security personnel because they only require a single line of code to be manipulated.
Sophos CTO Paul Ducklin said affected organisations risk losing business because they are flagged as malicious by search engines such as Google, and anti-phising software.
"You could imagine the business lost if one of only three or four local sign writers were tagged in a search as malicious," Ducklin said.
"It can be very expensive to fix iframe attacks because they can originate externally or internally, and they have a very small footprint."
Compromised Web sites can turn into virtual breeding grounds for further attacks, according to Ducklin, because they are easy targets for hackers wanting to inject additional malicious IFRAMES.
A 2007 Sophos survey found that more than 80 percent of Web sites listed as malicious were legitimate organizations that had been compromised by various attacks including iframe injections.
Ducklin said Sophos "tries to be fair" and revisits Web sites to see if they are still carrying the exploits, but could not specify exactly how long businesses remain blacklisted by security vendors or search engines.