The move had been expected, and the one-year tag will be worth in the neighborhood of $10 million, which was the average of the five highest-paid linebackers from the 2010 season.
Harris, who made a base salary of $550,000 in the final year of his rookie deal, was voted the Jets' MVP by his teammates after having 99 tackles and three sacks in his fourth season.
General manager Mike Tannenbaum recently said re-signing Harris was a priority, and the Jets still could lock him up to a long-term deal once the NFL's uncertain labor situation is cleared up despite placing the franchise tag on him.
Because he received a non-exclusive tag, Harris can negotiate with other teams. If Harris receives an offer, the Jets can either match it or receive two first-round draft choices from the other team as compensation.
A person with knowledge of the situation indicated to The Associated Press last week that the Jets were leaning toward using the designation on Harris, who is a valuable signal-caller in the middle of coach Rex Ryan's aggressive defense. Since being a second-round pick out of Michigan in 2007, Harris has 428 tackles, 15 sacks, five forced fumbles and two interceptions.
Harris will be the last of the team's "Core Four" players -- including Darrelle Revis, Nick Mangold and D'Brickashaw Ferguson -- to receive a new contract. The other three players were given new deals before the season, and Harris acknowledged in August that he wouldn't get his until after this season because of constraints due to the collective bargaining agreement.
"It's out of my hands and a lot of other people's hands," Harris said before the season. "That's the rules, and you've got to live by them."
Teams were able to start using the franchise label on Feb. 10, but it's still uncertain if the tag will stand because of the labor situation. Jeff Pash, the NFL's lead labor negotiator, recently said he expected the franchise tag to continue to operate as it has previously. But NFL Players Association executive director DeMaurice Smith said the 2011 season doesn't fall under the current CBA that expires March 3.
The Jets were busy during last year's offseason -- making a series of high-profile signings, cuts and trades on their way to a second consecutive trip to the AFC Championship Game. New York again will have several players to address this offseason in addition to Harris, including wide receivers Santonio Holmes, Braylon Edwards and Brad Smith, and cornerback Antonio Cromartie.
More franchise tags will follow throughout the NFL. The league advised teams that they have until Feb. 24 to tag players. Several teams will wait until the deadline in an effort to negotiate new deals with the players they would otherwise tag.
The Associated Press contributed to this report