The Australian hit a rock near the end of the event's third stage, which broke the power steering and forced him to make emergency repairs before the start of the next test.
Atkinson and his co-driver Stephane Prevot worked frantically to contain the time loss and to replace a damaged bolt in the steering.
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"I don't know where the rock came from," said Atkinson, who is deputising for Khalid Al Qassimi in Citroen's Abu Dhabi-branded car. "I think it had tumbled down off a fairly steep wall.
"I was following a pretty tight line through the corner, maybe a bit tighter than the other guys, but then we hit it.
"I thought we'd get a puncture - I wish we had, we were only a kilometre from the finish.
"Just before the start of the next stage, I gave it some gas to make sure it was OK and something broke. Luckily, we hadn't gone into the control, so we worked to fix it.
"A bolt was bent in the steering, so I had to whack that to straighten it to get it out and then we had to drive the rest of the morning with no power steering."
Atkinson is chasing a regular return to the World Rally Championship and possible further outings with the Citroen team. He is now in 11th place and is sure all is not lost.
"We're five minutes behind right now," he said. "I've finished third here and been five minutes behind...
"I reckon I could get back to fifth with a clean run to the finish.
"This thing's definitely not over. OK, we dropped a lot of time, but we could have been out and coming back with half an hour of penalties."