The league's board of governors had previously voted to set up a new alignment next season that would have divided the teams into four conferences. League officials then began meeting with the players to try to sell the plan, but those attempts were unsuccessful.
A union statement released Friday said the NHL never properly addressed concerns by the players after submitting the plan for their approval.
NHL Deputy Commissioner Bill Daly said in a statement that the league believes the players' union "acted unreasonably in violation of the league's rights." He said the league would evaluate its legal options.
"It is unfortunate that the players have unreasonably refused to approve a plan that an overwhelming majority of our clubs voted to support, and that has received such widespread support from our fans and other members of the hockey community," Daly said.
"We have now spent the better part of four weeks attempting to satisfy the union's purported concerns with the plan with no success. Because we have already been forced to delay, and as a result are already late in beginning the process of preparing next season's schedule, we have no choice but to abandon our intention to implement the realignment plan and modified playoff format for next season."
The board of governors voted on the realignment plan Dec. 5.
"In order to evaluate the effect on travel of the proposed new structure, we requested a draft or sample 2012-13 schedule, showing travel per team," the union said in its statement. "We were advised it was not possible for the league to do that.
"The travel estimation data we received from the league indicates that many of the current Pacific and Central teams that have demanding travel schedules under the current format could see their travel become even more difficult.
"We continue to be ready and willing to have further discussions."
A move to realign the league was made after the franchise that had been in Atlanta moved this season to Winnipeg. The Winnipeg Jets remained in the Southeast Division with Florida, Washington, Tampa Bay and Carolina for the 2011-12 season, thus creating a travel burden.