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Microsoft’s Steve Ballmer and Cisco’s John Chambers.

On the eve of Microsoft’s first-ever Lync Conference, Cisco today launched a campaign questioning Microsoft’s strategy of making its communication and collaboration products work “first and best” on Windows.

Cisco, which makes the WebEx collaboration and conferencing service, cites the rise of Android and Apple devices as evidence that Microsoft’s approach is increasingly out of touch. Cisco commissioned a survey of 3,320 IT leaders from nine countries, saying that nearly three-quarters of respondents thought Microsoft’s approach will have at least some negative impact on their business.

Cisco has been a Microsoft partner over the years, but Cisco opposed Microsoft’s Skype acquisition, and the two companies have become increasingly competitive.

“Our own statistics highlight why being device and operating system agnostic is crucial,” writes Cisco’s Carl Wiese. “The latest numbers we’ve recorded show there have been 3.7 million downloads of the Cisco WebEx Meetings mobile app for smartphones and tablets. We’ve seen 72% year-over-year growth in application downloads on Apple devices and 248% year-over-year growth for Android devices. While a (Bring Your Own Windows Device) world might be good for Microsoft, IT leaders know that it’s not good for business.”

Cisco points to a New York Times story quoting Microsoft CEO Steve Ballmer: “We always want Skype to be first and best on Windows, but certainly a strategic part of the value in communications software is working on all platforms.” Cisco contends that cross-platform support should come first.

On the other hand, just last week, Skype debuted a new video messaging feature for pretty much every platform except Windows.

No response yet from Microsoft to the Cisco campaign. Microsoft’s Lync Conference starts Tuesday in San Diego. The opening keynote by Skype’s Tony Bates will be available for viewing here at 9 a.m. Pacific.

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