Earlier this week, the company confirmed that it had accessed the Hotmail account - which Microsoft owns and operates - of a French blogger to obtain evidence about leaks.
It had been alleged that a former Microsoft employee had leaked confidential copies of the Windows 8 operating system before it was released to the public. The incident, which occurred in 2012, has since been investigated by the FBI over claims of theft of trade secrets.
In a statement, the company said it has adjusted its policy for dealing with future incidents like this, using an independent legal team to analyse whether or not they had the right to search through personal accounts.
"Courts do not issue orders authorising someone to search themselves, since obviously no such order is needed," it said. "However, even we should not conduct a search of our own email and other customer services unless the circumstances would justify a court order, if one were available."
Microsoft then outlined the new practices they will use in future, including the introduction of an external legal team to analyse any potential cases.
The statement then explained how evidence will be passed to an outside lawyer who Microsoft said is a former federal judge, and that the PC developer will not proceed unless the attorney concludes a court order would be attainable.
The company has been heavily criticised for the incident, especially in the wake of a series of advertising campaigns casting rival Google in a negative light for accessing customer data.
Vice president John Frank signed off the statement by re-enforcing Microsoft's belief that the corporation had acted correctly, but needed to work to keep customer trust.