Fyi, only file encryption with a third-party tool requires the public encryption key. File encryption with the Intel® Quartus® Prime Pro Edition software does not require the public encryption key.
Which third-party tool are you using?
As far as I know, each tool might have different way in using the public key. I suggest to refer to the third-party tool guide.
The encrypted code by default is readable in Intel® Quartus® Prime Pro Edition and there is no private key to decrypt the code.
Hope it helps.