The Barcelona forward was stretchered off with a back injury late in Brazil's 2-1 win over Colombia on Friday.
Neymar was taken to hospital after the heavy challenge from Juan Camilo Zuniga and Scolari said early signs were the 22-year-old would miss the meeting with Germany on Tuesday.
"Neymar is in hospital, with a lot of pain in his rib and he left crying," Scolari said.
"It's going to be difficult for him to recover in time for Germany."
Neymar's absence would be another huge blow to Brazil, who will be without captain Thiago Silva due to the centre-back's suspension.
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