An injury scare to the same hip that required career-saving surgery has left Rafael Nadal's Australian Open return up in the air.

The Spanish great's promising Brisbane International comeback was ended in a gruelling three-and-a-half hour quarter-final loss to Australian Jordan Thompson on Friday night.

Nadal had three match points in the second set but Thompson benefited from a handful of uncharacteristic errors and played brilliant tennis of his own to win 5-7 7-6 (8-6) 6-3 at a raucous Pat Rafter Arena.

The 37-year-old Nadal first grabbed at his upper left leg late in the second set, then at 1-4 in the third set and left the court for treatment as the match went into its fourth hour.

He returned to finish the contest, Nadal's third in four days and second in a row after almost 12 months without playing.

The 22-time grand slam winner had impressed while disposing of Dominic Thiem and Jason Kubler to reach the quarter-finals.

His fingers are crossed the injury concern amounts to nothing and he will line up at the Australian Open from next Sunday.

But he admitted his fear, given the proximity of the soreness to the hip that was operated on in June and which forced him off the ATP Tour after an early exit at Melbourne Park last year.

"Yeah, it is a very similar place to what happened last year, but different," he said post-match.

"I feel more muscle, last year was tendon.

"For sure it's not the same like last year at all because when it happened last year I felt something drastic immediately.

"Today, I didn't feel anything. The only problem is because the place is the same you are a little bit more scared than usual.

"I hope it's not important and I hope to have the chance to be practising next week and to play Melbourne. Honestly, I am not 100 per cent sure of anything now."

He said ideally it was just fatigue after back-to-back matches, a tip of the cap to 29-year-old Thompson who is set to return to the world's top 50 thanks to this Brisbane campaign.

"From this perspective you don't know all the information that I have," he told reporters.

"The only thing that probably you see is I have been playing very well the last two matches. It's true, I have been playing well.

"A lot of things can be happening in a body like my body, after a year without playing tennis.

"So hopefully it is just that, just a muscle that is supercharged ... if that's the thing, everything perfect."

"That's why ... I have been talking with a lot of precaution.

"If things happens, if I have one problem there, one problem to the other part of the body, I need to accept."