According to the analyst firm, the application's Search Across Computers option should be disabled or heavily managed by enterprises.
The warning comes after the search giant introduced the latest version of its desktop search application, formerly called Google Desktop Search, as the Desktop 3 Beta on 9 February.
Gartner research vice president Whit Andrews explained that the Google Desktop 3 Beta adds a variety of features, including the controversial Search Across Computers.
In essence, this feature allows PCs running the application to pool certain information and documents, a convenience that brings with it a "degree of risk" .
"Google's decision to use a remote server to hold a temporary index is inauspicious, but unique to its strategy. Google will store an index copy of information intended to be shared on its servers for up to 30 days," Andrews said.
"Google promises that this information will be encrypted and accessible only to a small set of Google employees, who will not peruse it.
"Nevertheless, Gartner believes that its mere transport outside the enterprise will represent an unacceptable security risk to many enterprises.
"Also, workers will not always reliably identify documents that must remain outside the category of shared items. Such decisions may be based on factors such as regulatory or security restrictions."
Gartner noted that Search Across Computers may be turned off for all workers in an enterprise through the management features of Google Desktop for Enterprise, the enterprise edition of the product.
Organisations using the enterprise edition are advised by the analyst firm to immediately disable this feature, and evaluate what they are allowing be indexed, and whether they are comfortable that they can adequately bar the sharing of data with Google's servers.
According to Gartner, enterprises that are not using Google Desktop for Enterprise and are allowing employees to use Google's desktop search application should start using the enterprise edition immediately and restrict its use accordingly.
Enterprises that have not selected a desktop search strategy are advised to provide a companywide default selection, including support and management, for willing workers.
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