With Barcelona 2-1 down in the tie, the players have decided not to make the trip just 48 hours before a Copa del Rey game.
Messi is nominated for the Best Player award and was also included in the team of the year with Andres Iniesta and Luis Suarez and the three of them were expected to attend the ceremony.
After a dressing room meeting on Monday, the players decided to stay back to instead focus on their crucial second leg last 16 Copa del Rey game against Athletic Bilbao.
With Barcelona 2-1 down in the tie, the players have decided not to make the trip just 48 hours before the game.
Despite the explanation, it is understood by many to be a snub to the award where his longtime rival Cristiano Ronaldo was honoured with the Best Player award.
It has also reported that Barcelona chose to shun the ceremony as a snub to FIFA after the decision by the court of arbitration to cut Real Madrid’s transfer ban in half.