England's numbers three, four and five -- Ravi Bopara, Ian Bell and Paul Collingwood -- contributed just 16 runs in the match which they lost by an innings and 80 runs to leave the series against Australia level at 1-1 going into next week's decider at the Oval.
"That was a very bad performance, it was bad from ball one," Flower told reporters. "We have to think about the middle order. We've got one ton in this series -- Andrew Strauss is holding us together."
Bopara is under particular pressure having failed to reach fifty in the series.
"Ravi Bopara has had a hard time," Flower said. "He was very confident coming in, but he's taken some knocks."
Bopara looked to have cemented his place in the team after making three centuries in a row against West Indies this year but he has struggled badly against the Australians.
England called Jonathan Trott into the squad for the Headingley Test and he could make his debut at the Oval.
"When Bopara came in and scored three tons he looked good, composed, certainly talented enough, but the jury was still out about whether or not he was a number three," Flower said.
"Trott was the next middle-order player that I, Strauss and the selectors thought would come in. He's in good form, he's been in the set-up before."
Flower said England would not be panicking.
"I don't want to look back and pick every single decision we made to pieces," he said.
"I don't think we're in disarray, we're 1-1 with a chance to win. Let's let this poor result settle and then we'll make decisions.
"It'll be a good Test wicket at The Oval, if we play really well, we'll win the game. We took 20 wickets at Lord's on a good deck, we can do it again."
Flower said he is hopeful all-rounder Andrew Flintoff would be fit to return to the team after missing the Headingley test.
"If he's there it'll be great to have a world-class all-rounder around, if not we'll have to do it without him," said Flower.
"I don't want to put a percentage on his fitness, but he must be ready to bowl at least 15 overs a day."