Users have complained that the company's latest tablet gets too hot to touch and its fan occasionally becomes loud.
The Surface Pro 3 has an Intel Core i7 chip, which "calls for the fan to spin more regularly and at higher speeds -- and for the unit to run slightly warmer," the company said in a statement.
But Microsoft said a small number of the devices are restarting themselves and showing a temperature gauge icon while booting up.
"Our investigation reveals that the system is triggering this event sooner than it should for some people, only when the device restarts, and this does not occur when the device is booted and running," it said.
An update will be released as soon as possible, Microsoft said.
Microsoft has high hopes for its Surface Pro 3, which it released in June, as the company has battles for a share of the crowded tablet market against Apple and a bevy of Android devices from a variety of manufacturers.
The Surface Pro 3 is a tablet that can be attached to a keyboard, a kind of hybrid device that could appeal to those in the market for either a tablet or a slim laptop.
Microsoft took aim at Apple in an advertisement, highlighting the Surface Pro 3's touchscreen feature, which Apple's MacBook Air doesn't have.
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