"It happened after there was a scuffle in the upper tier of the West Stand. A Liverpool supporter had bought a ticket off a tout and was in our end.
"At one point a fight broke out, he got up and thumped someone. Other people jumped in and stewards took him away. That started it all off.
"Liverpool fans saw one of their own taken off and tried to get on to the pitch." There were nearly 3,000 fans in the away end and as the trouble flared a disabled supporter was knocked over.
Police detained two fans from each team and several were ejected.
But Paphitis defended the behaviour of the Millwall supporters. He said: "When I saw this Hillsborough angle it was a shock to me.
"If it happened of course it is not acceptable. I would not condone it.
"But our fans did not try to get on the pitch. One thing they have learned is that we do not go on the pitch or fight with other fans. They have shown they will not cross the barrier.
"I will never defend the indefensible but I will not have Millwall fans berated when another team comes and causes trouble."
Paphitis accepted that it was not the first time trouble had flared at The Den after Millwall allowed fans into the bottom tier of the away end. He added they would review the arrangement.