Cofee is designed to offer police and other agencies a way of collecting digital evidence, decrypting passwords and analysing computer and web surfing activity.
The assurances came after reports claiming that Cofee could provide a 'back door' into Microsoft operating systems and applications.
In its Gartner briefing, however, Microsoft stated that Cofee offers nothing more sinister than a set of scripts designed to help law enforcement professionals take a system snapshot.
Microsoft claimed that the commands held on the USB stick are all public, and that no new code has been written and no back doors are present.
"Gartner believes, and Microsoft agrees, that it was a mistake to widely deploy the Cofee initiative without public disclosure and a formal distribution plan," said John Girard, a vice president and distinguished analyst at Gartner.
"We also believe that Microsoft should work closely with professional third-party forensics product and service vendors to develop, manage and track future data capture utility projects.
"Another concern raised by Microsoft's failure to offer public information about this initiative is that the widespread attention it has drawn will likely encourage otherwise well-intentioned enterprise IT personnel to search the internet for penetration tools with which to experiment.
"Enterprises should review their internal protection measures to ensure that their business data is secure and private."