Defeat in the Carling Cup to the League One strugglers, Gillingham, left the Pompey chairman, Milan Mandaric, with a face like thunder - reviving memories of the FA Cup exit to Leyton Orient which was the prelude to Graham Rix's sacking three years ago.
Perrin came in for the last seven games of last season following an ill-fated spell in charge by the director of football, Velimir Zajec.
But the Frenchman, despite making 12 new signings during the summer, has tasted victory just three times and admitted the Gillingham humiliation was his worst moment yet.
Although Portsmouth look relatively comfortable in 13th place in the Premiership, they have not yet faced one of the top teams, their only win being courtesy of a Duncan Ferguson own goal at Everton.
They must now pick up points from their next six League fixtures - against Bolton, Newcastle, Middlesbrough, Charlton, Sunderland and Wigan - before they confront Liverpool, Chelsea and Manchester United in consecutive games from late November.
At Gillingham, Pompey scored two goals in a game for the first time this season, Gary O'Neil and a Matt Taylor penalty twice putting them ahead. But Darren Byfield took advantage of goalkeeping blunders by Jamie Ashdown to level matters and after substitute Svetoslav Todorov missed a late penalty, Andrew Crofts struck an extra-time winner.
"Gillingham wanted to fight and we did not have the confidence to fight with them," said Perrin. "I have not spoken to the players at any length, but they should know why they lost, even though it was incredible."
Perrin accused his side of throwing the match away but he has done little to improve cohesive play by using seven different strike combinations this season.
Fans were bemused when the impressive Uruguayan Dario Silva was taken off at 2-2 only for his replacement, Todorov, to miss a penalty. It should have been his first goal since May 2003 when he clinched promotion. Since then he has fought a long battle to recover from two knee operations.
Now Perrin has to decide whether to recall Lomana LuaLua for Saturday's trip to Bolton after claiming it was flu which kept him out of the cup tie. It is an open secret, however, that LuaLua damaged a shoulder in a rough-and-tumble team-bonding exercise the manager instigated last week.
Laurent Robert will certainly return after being rested and Perrin added: "LuaLua can create things on his own, but we should have beaten Gillingham without him and Robert.
"I know the fans were upset with me but their reaction was normal. They travelled and expected to win a game like this. Everybody is disappointed."
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