The Blues boss claimed that there had been incidents leading up to Pompey's first two goals and that David Murphy's sending off for two bookable offences had alsobeen very harsh.
"I have not been as angry with any other refereeing performance this season. I know how difficult their job is to do, but the performance of the referee changed the course of the game. I went and saw him afterwards," Hughton said after Tuesday night's game at Fratton Park.
"We should have been given a free-kick in the run-up to their first goal and for their second there were five or six of my players claiming for a handball.
"Then the sending-off was for something so minimal. We left ourselves open for the third and fourth goals but at 2-1 down with 10 men it is always going to be difficult.
"We have got to pick ourselves up and forget about this game and keep fighting for a play-off spot."