Thompson said the security industry in general, and Microsoft in particular, are currently unable to deal with security threats and must take drastic steps to regain the confidence of the market.
Speaking immediately after Bill Gates, Thompson said that while he applauded Microsoft's efforts, "they will not be sufficient."
In particular, he said Microsoft's exclusive focus on the Windows platform was a weakness in a market where customers need to tackle security risks across their entire environment in a consistent manner. Microsoft's technology "is not cross-platform, and may be genetically unable to be so," he said.
Thompson called for a shift to being able to react technologically in unison to address a threat.
"We've got to develop infrastructure that actively resists threats and rapidly recovers from incidents," he said. He warned that this will require much greater interoperability from vendors than they have previously offered.
The Slammer virus had highlighted the fragility of the security industry, he continued.
"Slammer did not even have a malicious payload," he said. "It gave us a foreshadowing of what is to come."
Critics suggested Thompson's offensive was due to Microsoft's imminent entry into the consumer anti-virus marketplace.