And considering how intertwined universities are with other organizations—including government agencies—it's likely a university breach could put other critical organizations in jeopardy, Boyer said.
"It's really important to realize that cybersecurity is a systemic problem," he said. "We are all on the same network, problems in one area can lead to problem in another, especially in universities."
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Malware, or malicious software, infections are among the biggest threats on college campuses. Flashback to the Trojan horse virus, which targeted Apple computers and stole personal information by disguising the virus as a browser plug-in. Such Trojan-like viruses are the most prevalent type of malware on college campuses, according to the report.
Other prevalent malware found on university networks include Adware, a kind of malware that targets users through online ads. Other persistent malware includes Conficker, which is a computer worm that targets Microsoft Windows operating system.
Boyer noted that schools with the highest scores had a dedicated director of information security or a chief information security officer on staff.
—By CNBC's Cadie Thompson