The PFA team is voted for by the Premier League players themselves and included six Chelsea players, including Branislav Ivanovic, John Terry, Gary Cahill, Nemanja Matic, Eden Hazard and Diego Costa.
David de Gea (Manchester United), Ryan Bertrand (Southampton), Phillippe Coutinho (Liverpool), Alexis Sanchez (Arsenal) and Harry Kane (Tottenham) made up the rest of the team.
“There should have been more Chelsea players. All of them should have been Chelsea,” he said.
“I respect every player in that team and especially everyone that chose because they have the right to choose.
“Great players are in that team but also eight players are outside that team.
“Just one example is Cesc Fabregas, with the season he is having, the number of assists, the quality of his game. For him not to be there is strange.
“And that team wouldn’t win the Premier League. It has four defenders, Matic, and five to attack so it’s impossible.
“It’s a team without any balance and it is missing a midfield player.”
In addition to dominating the team of the year, Chelsea midfielder Eden Hazard was also rewarded with the PFA Player of the Year award in recognition of the season he has had.
Mourinho expressed his happiness for the player, but stressed the team’s achievements were more valuable than individual accolades.
“It’s more important for us to be champions but this is nice,” he said.
“Obviously I’m happy for him and I’m happy for every player that helped him to achieve the level he’s achieving this season, which made him win the Player of the Year.”