The Finnish driver managed just six laps before he retired, with reports suggesting his turbo overheated.
His session was in stark contrast to that of his teammate Sebastian Vettel who led from the front from a time of 1:32.697, ahead of Daniel Ricciardo and Max Verstappen.
It has been a mixed start for Raikkonen as he has seen Vettel win the opener in Australia and finish second last weekend in China.
Although the 37-year-old finished both races in 5th, he is already 21 points behind Vettel and Lewis Hamilton, who are joint leaders with 43 points.
After the race in China, he said: "I think we could have, should have had a better result - but this is what we got today. I think we should have changed earlier, but obviously it's easy to look at what happened and say after the race.
"The car was good when the tyres were fresh, but it seemed to lose the front and at a place like this, you give a lot of time away and struggle to drive.
"I feel we should have done much better..."
— Formula 1 (@F1) April 14, 2017
It raises questions as to why Vettel did not have any similar problems and why the team didn’t prepare the car properly with the temperature in Bahrain just under 40 degrees Celcius.
Raikkonen is usually very forthright with his opinions and it is likely he was asking several questions as his SF70-H was being taken apart after the session.
Lewis Hamilton finished 10th, 1.9 seconds off first.