The order by the U.S. International Trade Commission has been sent to President Barack Obama, who has 60 days to consider whether to overturn it for policy reasons.
The legal fight at the ITC is one of dozens globally between various smartphone makers. Google's Android system has become the top-selling smartphone operating system, ahead of mobile systems by Apple, Microsoft, Research in Motion and others.
On Wednesday, some of HTC's smartphone models were stopped at the U.S. border because it lost a patent dispute with Apple at the ITC in December. Shares in HTC tumbled more than 6 percent on news that shipments of the phones were being held up by U.S. customs.
The ITC order did not say which models of Motorola Mobility smartphone were affected but Microsoft has asked for the following devices to be stopped at the U.S. border: the Atrix, Backflip, Bravo, Charm, Cliq, Cliq 2, Cliq XT, Defy, Devour, Droid 2, Droid 2 Global, Droid Pro, Droid X, Droid X2, Flipout, Flipside, Spice and the Xoom tablet.
The patented technology at issue makes it possible for users to generate meeting requests and schedule gatherings using their mobile devices.
One option for Motorola Mobility will be to remove the meeting-scheduling technology from its smartphones and tablets. The company could also license it from Microsoft.
Motorola Mobility, which is in the process of being acquired by Google, said the company would not feel any near-term impact.
"Although we are disappointed by the commission's ruling that certain Motorola Mobility products violated one patent, we look forward to reading the full opinion to understand its reasoning," the company said in an emailed statement. "We will explore all options including appeal."
Both sides can appeal to the U.S. Court of Appeals for the Federal Circuit.
Microsoft said it was pleased with the decision. "We hope that now Motorola will be willing to join the vast majority of Android device makers selling phones in the US by taking a license to our patents," a company spokeswoman said via email.
In a complaint filed in October 2010 with the ITC, Microsoft accused Motorola Mobility of infringing nine patents for Windows Mobile and Windows Phone.
Two patents were dropped during litigation. An ITC administrative law judge in December found that Motorola Mobility infringed on one Microsoft patent in making Android cellphones but did not infringe on six others.
Google's Android software has recently become the most popular cellphone operating system with 56 percent of the market in the first quarter of 2012, according to data from Gartner Inc.
Motorola, which makes Android phones, is one of the smaller mobile phone makers with 8.4 million units sold globally in the last quarter, according to Gartner.
The ITC is a popular venue for patent litigation since it has the power to forbid the importation of products that infringe on patents.
The case at the ITC is No. 337-744.
(Reporting By Diane Bartz; Editing by Tim Dobbyn, Gary Hill)
By Diane Bartz