Hal Robson-Kanu, Rabbi Matondo and Tyler Roberts have been released from the Wales squad after "breaching protocols".
BBC Sport Wales has learned the breach is not Covid-19 related, but applies to rules covering squad discipline.
Wales are preparing for Tuesday's World Cup qualifier against Czech Republic in Cardiff.
"The three players will be returning to their respective clubs this afternoon," said the FAW.
"The FAW will not be making any further comment."
Leeds United forward Roberts apologised and accepted his banishment, stating: "Gutted to be leaving the camp early, but rules are rules and I shouldn't have been up in the hotel later than the set time.