The 18-year-old sustained the injury playing for Wales' Under-21s against Armenia on Tuesday night.
"We're still awaiting further news," Eagles boss Dougie Freedman told the club's official website.
"It's obviously very sad for the young man and his family first of all. But knowing Jonny, he's a very positive person with a lovely family to support him. He's got the club's backing in terms of giving him the best medical care he could get.
"These things, setbacks, happen in life, not just in football, but knowing the person and the family I think this young man will cope with it very well and probably come back better physically as well as mentally.
"It's sad news but you will see Jonny Williams' character coming through and he will be back in a Palace shirt."