Steven Martin, senior director of developer platform management at Microsoft, said in a blog post that the document is biased to benefit its authors - some of whom are also Microsoft's competitors.
"From the moment we kicked off our cloud computing effort, openness and interoperability stood at the forefront," he wrote.
The 'Cloud Manifesto' apparently describes various principles and guidelines for interoperability in cloud computing.
However, while Martin said that Microsoft "loves the concept" and "strongly supports" an open and collaborative discussion with customers, analysts and other vendors, he is disappointed that the Manifesto has been developed with a lack of openness.
"What we heard was that there was no desire to discuss, much less implement, enhancements to the document, despite the fact that we have learned through direct experience," he said, adding that Microsoft considers standards and interoperability key to the long-term success of the industry.
Martin alleged that Microsoft was privately shown a copy of the "secret" document and told to sign it 'as is', without being allowed to add any modifications or make any additional input.
Martin said: "It appears to us that one company, or just a few companies, would prefer to control the evolution of cloud computing, as opposed to reaching a consensus across key stakeholders [including cloud users] through an 'open' process.
"We are happy to participate in a dialogue with other providers and collaborate with them on how cloud computing could evolve to provide additional choices and greater value for customers."
Martin added that Microsoft believes that interoperability principles and standards for cloud computing need to be defined through a process that is open to public collaboration and scrutiny, and should not be a vendor-dominated process.
He went on to say that the cloud market is still "immature", and that "a great deal of innovation" is yet to come.