Cleary's upper right leg emerged as one of the key talking points of State of Origin II, after he did not kick goals and had his thigh bandaged.
The issue prevented Cleary from goal-kicking and putting up long kicks in general play during the first half on Wednesday.
It proved pivotal with the wayward boot of replacement goal-kicker Zac Lomax ultimately proving the difference between the sides in a 26-24 loss for NSW.
On Thursday morning, Cleary revealed he had injured himself while goal-kicking at Tuesday's captain's run but never felt the issue was serious enough to sideline him.
"I always thought it would be fine, it was just sort of the kicking load which was up in the air," he said.
"I don't actually know the exact thing (injury) but I essentially did it goal-kicking in captain's run. It's a little bit frustrating.
"I can't commend the physios enough, they put a lot of time into me at captain's run and the morning of the game."
Cleary is already set to be rested from Penrith's clash against the Warriors in Auckland due to travel, with the Panthers not backing up any of their five Origin stars.
But his fitness after that is crucial with Penrith attempting to revive their season and an Origin decider just three weeks away.
NSW have already lost first-choice five-eighth Mitch Moses to a calf injury, with Jarome Luai called in to wear the No.6 jersey on Wednesday night.
If Cleary was to be in some doubt, Matt Burton would loom as the most likely option to come into the Blues' side for the July 9 decider at Accor Stadium.
AAP has been told Cleary did not require scans in the lead up to Wednesday's match and had been in close contact with Penrith and his father Ivan.
The halfback is not expected to undergo scans when he flies home to Sydney, and not scheduled to return to the Panthers until Monday.
"Obviously he is a massive part of both teams," Penrith and NSW second-rower Liam Martin said.
"I am sure he will be fine. He will do everything he can to be sweet and I'm sure he will be."
At full-time, NSW coach Laurie Daley took the blame for the Blues' first-half flop and indicated he'd remain loyal to his players for the series decider in Sydney.
The Blues gave away eight penalties in the first half alone, completed at 56 per cent and had their defence pulled apart with 22 missed tackles.
NSW scored four unanswered tries in the second half as they threatened to pull off the greatest comeback in Origin history.
But Lomax's three missed conversions and the team's horrific first half was left to haunt them.
"I've got to take responsibility, because we started well (with the first try), but the first half wasn't great," Daley said.
"So I've got to look at what I've done, because something isn't right."
Daley was protective of his players when asked if he was confident in his current squad or would need to make changes for game three.
"Well, I was confident at half-time," Daley said.
"I know what this group is capable of, and that's the thing you get disappointed with, because they never gave themselves that opportunity.
"You can't play a half of football like that against quality opposition and expect to be close.
"So for us, it's a good lesson. We'll go back to the drawing board.
"It's one-all. That's what Origin is all about, and it creates theatre and it creates headlines.
"I'm sure everyone wants a decider, and they've got it now."
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