The warning comes in the wake of Kaspersky Lab filing an anti-trust complaint against the software giant last year.
Kaspersky has filed similar cases with the European Commission and Germany's Federal Cartel Office against what it calls Microsoft's abuse of its dominant position in the operating system market and its unfair competition in the anti-virus market.
On Wednesday, Microsoft admitted that it had disabled some third-party anti-virus software at the time of the Windows 10 Creators Update due to compatibility reasons, though it did not mention any vendor by name.
The FAS said Microsoft should act to change the alleged restrictions it imposed on users of anti-virus software from third parties.
It also called for what it said were changes in the ways used to disable anti-virus software and prevent their being updated. The company was told to rectify what FAS called the complicated procedures that were needed to update third-party anti-virus software.
Microsoft was also warned about its alleged failure to ensure timely two-way communication.
The FAS also claimed that Microsoft may have violated the anti-monopoly legislation by employing certain methods inducing users to stop using anti-virus programmes made by third parties and to activate software made by Microsoft (Windows Defender).
Commenting on the FAS notice to Microsoft, Nadezhda Kashchenko, chief intellectual property counsel at Kaspersky Lab, told iTWire: "In this matter, Kaspersky Lab's main objective is to provide people with the ability to choose the most reliable, high-quality protection against all types of cyber threats.
"We are pleased with the FAS decision because first and foremost, it will have a positive effect on users. If Microsoft reconsiders its actions in accordance with the warning, users will be able to make an informed choice when selecting a cyber security solution without unfair outside influence.
"This will also have a positive impact on the security solution market, as it will ensure a level playing field for all vendors and contribute to healthy competition."
Microsoft has been contacted for comment.