Brawn GP team principal Ross Brawn described the team's qualifying performance as "disastrous" after Rubens Barrichello and Jenson Button qualified 10th and 12th for the Singapore Grand Prix.
Button was knocked out in Q2, while Barrichello ended up fifth after bringing the session to an early halt by crashing.
He has also had to take a five-place grid penalty for changing his gearbox after just two races.
"It was a disastrous sessions," Brawn told BBC Sport. "We underestimated the competition in Q2 and used one set of old tyres and then one new set and we didn't get the car balanced well on the new set.
"We were perilously close to losing both cars in Q2. Q3 wasn't bad when you see the fuel weights, but it topped off a bad session for us.
"It's not a great day for the championship. We'll have to tough it out and try and see what we can recover tomorrow."
Brawn confirmed that the gearbox change on Barrichello's car had been made as a precaution.
Despite being used in both the Belgian and Italian Grands Prix, the unit suffered an over-torque at the start at Spa, with tests at the team's Brackley base suggesting that it could have problems if used in tomorrow's race.
"We've been running a gearbox on the dyno at the factory in parallel and we saw some worrying signs when it got up to its third race. It's quite a hard track on gearboxes although I'm not sure that one survive because it hit the wall pretty hard."