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"We need legal approaches, we need prosecutions, we need education that make sure we get the same protection, whether it's personal assets or corporate assets or national asset that people expect," he told a London School of Economics audience in London.
"That's not going to be an easy challenge, no question about it," he said. "We are hard at work about it, as are nation states. Governments in most parts of the world really get this."
Ballmer described society's increasing reliance on IT as crucial as it brought into focus wider issues such as privacy.
"The degree to which a society makes an agreement of the way things work onto the back of (IT) infrastructure is a big deal," he said.
He called for governments to harmonise legislation and procedures with respect to the social impacts of IT. This would speed up development, but Ballmer warned not to expect this any time soon.
"If we could get a harmonisation between Europe the US and China, we could at least get a framework that allows innovation to proceed," he said.
Stuxnet is a Trojan that targets Windows-based superviory and control equipment made by Siemens. Such equipment usually bruns with minimal human intervention. Stuxnet can take over the system and cause it to malfunction. Iraq has admitted that Stuexnet infected systems that contolled its commercial nuclear reactor, but have not said whether it damaged the reactor.