The document, known as the Microsoft Global Criminal Compliance Handbook, describes the company's methods for storing private data and how law enforcement agencies can gain access to millions of accounts.
Cryptome was shut down by its hosting provider, Network Solutions, last week after complaints from Microsoft that the site had infringed its copyright.
Under US copywriting laws, any hosting site will be immune from legal prosecution if the offending content is taken from a site during the time when a counter-claim is being considered in court.
The 22-page document specifies the types of information Microsoft gains from its users from various services including Windows Live, Xbox Live and instant messaging client MSN Messenger.
However, Microsoft legal counsel Evan Cox said in a statement the company did not intend to shut down the whole site.
"While Microsoft has a good faith belief that the distribution of the file that was made available at that address infringes Microsoft's copyrights, it was not Microsoft's intention that the takedown request result in the disablement of web access to the entire cryptome.org website."
"Accordingly, on behalf of Microsoft, I am hereby withdrawing the takedown request and asking that Network Solutions restore internet access to http: cryptome.org as soon as possible."
Nevertheless, Cryptome said the subsequent outcry from civil liberties campaigners, which caused the site to reappear, was a big win for freedom of information. Proprietor John Young said in a statement the company needs to be more open about its procedures for gathering and allowing access to information.
"We think all lawful spying arrangements should be made public," he said. "Microsoft should join the others who openly described the procedures, and just maybe do if there is a public demand for it."
Additionally, Young said the handbook itself was "repugnant" for allowing, and even encouraging, law enforcement authorities to monitor private information.
But the company did not apologise for the existence of the document, and said it was necessary as part of the company's involvement with law enforcement. It stated the document clearly presents that subpoenas, court orders and search warrants are required to access any information.
"Like all service providers, Microsoft must respond to lawful requests from law enforcement agencies to provide information related to criminal investigations. We take our responsibility to protect our customers privacy very seriously, so have specific guidelines that we use when responding to law enforcement requests."
Cryptome, which is similar to the recently shut-down Wikileaks, has previously released similar documents for sites such as Facebook and Yahoo. It has successfully avoided other shut-down attempts from organisations including the Recording Industry Association of America.
It describes itself as a haven for "documents for publication that are prohibited by governments worldwide, in particular material on freedom of expression, privacy, cryptology, dual-use technologies, national security, intelligence and secret governance but not limited to those".
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