Neil Harris apologised to Bradford boss Stuart McCall after a number of Millwall fans stormed the pitch after the League One play-off final.
Experienced striker Steve Morison was the Lions’ hero at Wembley, scoring a late goal to send Harris’ side back into the Championship.
After the final whistle, hundreds of Millwall supporters ran on to the pitch – with some confronting McCall and his Bradford players.
When asked about the unsavoury scenes, Harris said: "I don’t think it’s the place for that [Wembley].
"I don’t condone it and I would certainly like to apologise to Stuart, his staff and the players for the fans coming on.
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"I’m hoping they came on in good nature so I don’t condone it – but it won’t take away my joy tonight."
On his side’s performance at Wembley, Harris added: "I’m a happy manager today. I’m delighted with the character, not just today, but throughout the season.
"To bounce back from last year, with difficult spells throughout the season, shows the enormous spirit and desire in the camp.
"When we’ve needed a performance, and a moment, my players have delivered."
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