Left-handed reliever Boone Logan is also eligible. The trio of Yankees hurlers was offered contracts for the 2011 season in advance of the Dec. 2 deadline, but they have not yet agreed to those deals.
Hughes, 24, was an All-Star for the first time in 2010, going 18-8 with a 4.19 ERA in 31 games (29 starts), setting career highs in wins, losses, innings pitched (176 1/3) and strikeouts (146).
The youngest Yankees right-hander to win at least 18 games in a season since 23-year-old Mel Stottlemyre won 20 in 1965, Hughes earned $447,000 as he pitched in his fourth Major League season.
Chamberlain, 25, was 3-4 with three saves and a 4.40 ERA in a team-leading 73 appearances for the Yankees last year, working exclusively out of the bullpen for the first time in his professional career.
Projecting to continue in a relief role as the Yankees prepare to head to Spring Training and with a return to the rotation having been ruled out by club brass, Chamberlain earned $487,975 for his services in 2010.
Logan, 26, was 2-0 with a 2.93 ERA in 51 relief appearances for the Yankees in 2010, serving for most of the season as their lone left-hander in the bullpen.
Acquired before the season in a trade with the Braves, Logan earned $590,000 from the Yankees after agreeing to a contract offer, avoiding arbitration in his first year of eligibility. He figures to enter 2011 complementing Pedro Feliciano as the left-handers in the Yankees' bullpen.
In most cases, filing for salary arbitration is merely procedural. Chamberlain, Hughes and Logan can still come to agreements with the Yankees before their hearings, which would be scheduled to take place during the first three weeks of February.
Players have until Jan. 15 to sign with their clubs. Teams and players would then exchange salary figures on Jan. 18 in advance of the hearings.
The Yankees' last trip to arbitration was in February 2008, when they prevailed in their case against right-hander Chien-Ming Wang.
The Yankees avoided arbitration earlier this winter with right-hander Sergio Mitre, who signed a contract worth approximately $900,000 on Dec. 1. Mitre figures to compete for a starting role in the back of New York's rotation.
The Yankees also parted ways with right-hander Dustin Moseley, who was eligible for arbitration and later signed a $900,000 deal with the San Diego Padres.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.