"These are the vulnerabilities that can get you into trouble," said Jeremiah Grossman, founder at WhiteHat Security, the company behind the report. "They can compromise some or all of your systems, get user data, or take over accounts."
These are the kinds of vulnerabilities that need to be fixed quickly, before they make news headlines, he added.
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Retail sites ranked second in the number of vulnerabilities, with 55 percent of the websites having at least one serious vulnerability every single day of the year.
The worst performers Public administration websites, where 64 percent were vulnerable every day.
But this wasn't a simple matter of failing to keep patches up to date, Grossman said.
"One or two percent of the vulnerabilities are patchable," he said. "Most that we find are exclusively in the custom web application software."
To look deeper into why those vulnerabilities weren't getting fixed, WhiteHat conducted in-depth surveys with 118 customer companies, ranging in size from startups to the Fortune 50.
The single biggest factor was whether an organization's remediation efforts were driven by compliance reasons or risk reduction.
Those who focused on compliance had the lowest number of vulnerabilities, at just 12 per website. They also had the highest remediation rate -- the ratio of closed to open vulnerabilities during the time period studied -- at 86 percent.
Organizations primarily driven by risk reduction had an average of 23 vulnerabilities per website, and a remediation rate of just 18 percent.
One reason could be that companies that focus on risk prioritize the vulnerabilities and fix only those that fall into the unacceptable risk category.
Meanwhile, compliance-driven companies took longer to fix vulnerabilities -- 158 days compared to 115 days for risk-driven companies. This was possibly because they can afford to wait to fix the vulnerability until just before the next audit.
Another significant factor was whether vulnerabilities were put into a company's bug tracking system.
Vulnerability scans and penetration tests often come back in the form of reports, said Grossman.
"Someone has to transcribe it into the bug traffic system," he said. "But sometimes they'll just throw the report over the fence and just tell the developers to take care of it."
Organizations that have a process for putting vulnerability results into the bug tracking systems have, on average, 45 percent fewer vulnerabilities and increase their remediation rates by 13 points.
"When companies do that, it's probably the closest thing to a best practice that the industry has," said Grossman. "it seems to affect everyone extremely positively across all the major metrics."
Solving the problem requires that companies assign staffers to transcribe the vulnerability reports as they come in, or to work with the security vendors to have them put the results right into the bug tracking systems.
"At WhiteHat, we have an API to export the vulnerability data we find into XML," said Grossman. "Our customers have their bug tracking system programmatically wired, so it just flows automatically into the system and becomes part of the developers' work flow."