Spies was forced to miss his final two races of 2012 after a heavy crash in last year's race at Sepang left him with an AC shoulder separation, a cracked rib and bruising to the lung.
He underwent successful surgery and returned to MotoGP action in this week's test, only for a relatively minor Turn 1 fall to aggravate his injury.
"I made a small mistake yesterday which dug my elbow into the ground," he said.
"It was an easy crash but it upset my back and shoulder a little bit, so I had a few spasms yesterday and couldn't do a whole lot of riding."
After ending the final day 14th, and more than half a second off team-mate and MotoGP rookie Andrea Iannone, Spies admitted that his lack of fitness was hampering his speed.
"Anybody in our shoes would obviously like to be a little higher up the timesheets," he said.
"Today we rebounded a little bit and got to put some laps in, but had a couple of little problems with the bike and lost the last hour.
"All in all, it wasn't too bad and our quickest lap was actually set on old tyres - so that was good – but we'd like to be faster.
"For me right now, I just want to get back to 100 per cent fitness and get used to the bike."