We know that one of them is in Australia.
When Pottermore released the Wizarding School writings in January 2016, it was implied that their plan was to release the rest later (whenever Pottermore decided that they needed another traffic boost). One of them was going to be Australia.
The writings were first "unveiled" at HP Celebration 2016, where Evanna Lynch read three of them outloud. However, whoever wrote her introduction speech didn't seem to be aware that only some of the writings were being released.
What if I told you that there are Wizarding Schools in Africa, Brazil, Australia, Russia, and other secret locations? So this evening, for the very first time, I have the pleasure of reading to you brand new details about some of these Wizarding Schools.
Rowling also seemed to imply the same on twitter, when she was replying to tweets about the newly released writings.
where do aussie wizards go?
J.K. Rowling: That information will be revealed in due course!
One of them might be in Canada
Another of Rowling's tweets seemed to imply that there was a Canadian school as well.
What is the Canadian school of witchcraft and wizardry? I feel like Canadians are always left out
J.K. Rowling: Keep watching @Pottermore...
However, this may have just been referring to the Ilvermorny school, which hadn't yet been revealed at the time.
There is no information available about where the third "missing" school would be.
By the way, most of what we know about Koldovstoretz also came from leaked information. (A pottermore employee included it in a 2014 Pottermore fact list without realising the corresponding writing hadn't been published yet.)