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The Brno winner lost his Peugeot-badged Mahindra coming over the Lukey Heights crest on lap six at Phillip Island, which triggered a pile-up in the lead group and subsequent red flag.
McPhee's bike was collected by Andrea Migno and Enea Bastianini on the run to Turn 10, with the latter then hit by Jorge Navarro.
Bastianini sustained a fractured T9 vertebra and rib and is in doubt for this weekend's Malaysian Grand Prix.
McPhee will miss the Sepang race and, according to backer Racing Steps Foundation, "almost certainly" next month's Valencia finale.
He has a broken thumb and was diagnosed with a concussion, while an accumulation of air between a lung and the chest wall means he will stay in Melbourne rather than flying back to the UK.
"I'm feeling OK, bit stiff all over as expected but I'll be here in Melbourne for the next week or so as I've got a little damage to my lungs so need to keep an eye on them before I fly," McPhee wrote on social media.
"Hoping to have my thumb operated on in the next couple of days then be back to full fitness ASAP."
Currently 20th in the championship, McPhee has been linked with a switch to Honda machinery in Moto3 in 2017.
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