In a brief order, U.S. District Judge Jed Rakoff in New York said the lawsuit would proceed despite the arbitration. Rakoff said he would explain his reasoning in a subsequent opinion.
Microsoft sued Samsung in August, accusing it of breaching a collaboration agreement by initially refusing to make royalty payments after the U.S. company announced its intention to acquire Nokia's handset business in September 2013.
The lawsuit claimed Samsung still owed $6.9 million (roughly Rs. 42 crores) in interest on more than $1 billion (roughly Rs. 6,184 crores) in patent royalties it delayed paying.
Samsung has countered that the Nokia acquisition in April violated its 2011 deal with Microsoft.
Samsung filed the request for arbitration with the Hong Kong office of the International Court of Arbitration of the International Chamber of Commerce.
Samsung also agreed to develop Windows phones and share confidential business information with Microsoft, according to the filing.
Antitrust regulators in the United States and other countries approved the Nokia acquisition.
Samsung did not immediately respond to a request for comment. A Microsoft spokeswoman said the company was "pleased that the court agrees that New York is the appropriate venue for this dispute."
The case is Microsoft Corp vs. Samsung Electronics Co Ltd, U.S. District Court, Southern District of New York, No. 14-6039.
© Thomson Reuters 2014