New York Judge Jed Rakoff said the lawsuit would proceed despite the arbitration.
Microsoft sued Samsung in August, claiming it broke a collaboration agreement by refusing to make royalty payments after the US company announced its intention to buy Nokia’s handset business in September 2013.
The lawsuit claimed Samsung owed $6.9 million in interest on more than $1 billion in patent royalties it delayed paying. Samsung said that the Nokia acquisition in April violated its 2011 deal with Microsoft.
Samsung has gone to arbitration at the Hong Kong office of the International Court of Arbitration of the International Chamber of Commerce.
Samsung had agreed in 2011 to pay Microsoft royalties in exchange for a patent license covering phones that ran Google Android operating system.
Samsung also agreed to develop Windows phones and share confidential business information with Microsoft, according to the filing.
But once Microsoft acquired Nokia, it became a direct hardware competitor with Samsung, the filing said, and Samsung refused to share some sensitive information due to antitrust concerns.