After podium finishes for Lewis Hamilton in Malaysia and China, Brawn declared that Bahrain would be an acid test for Mercedes given that it had previously struggled at the track.
Although Nico Rosberg took a surprise pole position, he tumbled to ninth in the race, while Hamilton could only get up to fifth having been off the pace in the early laps.
Brawn acknowledged that this was an underwhelming performance in what he had billed as a crucial indicator of Mercedes' form, but believes the problems were entirely down to falling out of the ideal tyre operating window in the high temperatures.
"To be honest, we didn't anticipate quite such difficulty. It was worse than we expected," he said.
"We knew before we went there that if we could get on top of things there, it would be a pretty encouraging sign.
"But I think we're not far off because in the second half of the race when it cooled down a little bit, Lewis was able to pick the ball up and run with it again. He had certainly struggled in the first half of the race."
Asked if he felt Mercedes was beginning to repeat its 2012 downturn, in which it won in China then rarely got near the podium again, Brawn replied: "I think it's a little bit different. At least we had the core performance, we just overheated the tyres."
Brawn conceded that Mercedes was still marginal on tyres and risked similar problems whenever temperatures rose, though he believes Bahrain exaggerated the situation.
"We could have more races like that unless we improve our performance in this area, because if you're at one end of the scale, then whenever the tyres become compromised because of the temperature, you'll be the ones meeting that limit earlier than other people," he said.
"It might be that everyone's having difficulty, but it's a question of degree.
"It was reasonably encouraging at the start of the season because we didn't have those issues, and even in Malaysia we managed to find the right solutions.
"We just didn't find the right solutions in Bahrain; we didn't find the right pointers on Friday and Saturday morning to tell us how the race was going to go."
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