Heavy-handed stewarding and poor facilities will also be mentioned.
Paphitis was adamant his club's fans behaved well throughout the trip, but he hit out at Ferencvaros and their setup.
He said: "Even as a kid I cannot remember it being as bad as that.
"It was like going back into the dismal time of football that we all try to forget.
"It was all the things we have spent the last six years trying to put behind us and move forward.
"We could not leave our seats during the game due to the extra police who had to be summoned to protect us. A variety of things kept flying over. Anything from drink to coins and bits of food.
"When there are women and children there it is not on. It did get hairy at one stage and we missed about 10 minutes of the game because we had to turn around to deal with it.
"I also heard racial chanting and the delegate will be reporting it."
Paul Ifill and second-half substitute Mark McCammon were the main targets of widespread monkey chanting among the Ferencvaros fans, who have a reputation for racist behaviour and violence at games.
Striker McCammon said: "I heard the chants but you have to block it out and rise above it and I think I did that.
"It did not affect me and I don't want the club to complain officially. It was a game of football and their ignorance is their problem."
Millwall started reasonably but defended poorly at the start and were punished.
The home side had been practising aerial attacks all week and took advantage of some poor defending after 25 minutes when Denes Rosa was given a lot of space to head the first goal.
Botis Sorin was similarly unmarked when he headed in the second six minutes later off the underside of the bar, although there were muted claims from the visitors that the ball had not crossed the line.
Ferencvaros's third came five minutes before the break from a deflected Robert Wagner shot.
Dennis Wise gave Millwall hope with a neat close range goal just before half-time and his side never gave up the fight.
Sadly, however, the game will not be remembered for Millwall's brave display but for the ugly scenes off the pitch.
