"I didn't expect to, you know, to not continue here.
"But I think I'm going to evaluate what options do I have now... maybe just go right away to Melbourne."
Muguruza - the reigning WTA Player of the Year - had hoped to reclaim the world No.1 ranking she held for four weeks in 2017 by making the Brisbane final.
Instead the Spaniard was forced to withdraw from the Brisbane tournament for the fourth straight year due to injury.
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Muguruza said she felt her calves tightening early in the second set but dug deep to grab a break and lead 2-1 in the deciding third.
However, the Spaniard's match was over after she fell to the ground in agony grabbing her leg while attempting to make a backhand return.
She received medical treatment before deciding to pull the pin, ensuring Krunic became the first through to the Brisbane quarterfinals.
Krunic will next play Samantha Stosur's first round conqueror, seventh seed Anastasija Sevastova of Latvia, who downed Romania's Sorana Cirstea 6-2 6-1 on Tuesday.
"I don't really cramp a lot, so I'm actually surprised that today my body was like that," Muguruza said.
"It's a shame because I always come here excited about the first tournament, and this one was bad luck, I guess."
World No.38 and last year's Brisbane finalist Alize Cornet of France joined Krunic in the quarterfinals by downing Croatia's Mirjana Lucic-Baroni 6-1 7-5 on Tuesday.
In first-round men's action, Korea's Hyeon Chung upset fifth seed Gilles Muller of Luxembourg in straight sets and will next meet big hitting world No.50 Kyle Edmund of Great Britain who held out Canadian 18-year-old Denis Shapovalov 7-6 (7-5) 6-7 (4-7) 6-4.
Uzbekistan's Denis Istomin ousted seventh seed Damir Dzumhur of Bosnia-Herzegovina in three sets while American qualifier Michael Mmoh upstaged world No.68 Federico Delbonis of Argentina 6-3 6-4 to book a second-round clash with eighth seed Mischa Zverev of Germany.
- AAP