Hughes, who will be 36 in November, has represented his country 72 times and is currently the equal third-most capped player in Welsh history, alongside Peter Nicholas, and behind Ian Rush (73) and Neville Southall (92). But his decision to stand down for the next two games - he would certainly have played in both had Bobby Gould still been in charge - casts a doubt over whether he will ever represent his country again.
The FAW's secretary general, David Collins, said: "Mark has intimated to us that he will run the team from the bench and not play in these next two games."
If Wales manage to salvage a place in the play-offs for the European Championships, Hughes' two matches will have been a great success and he would therefore be unlikely to recall himself.
Should Wales fail to qualify, they would have just a couple of friendly matches before next summer and Hughes' chances of being included by a new manager would not be great.
Hughes' appointment has received approval from the former Wales captain Barry Horne. "His experience is second to none as a player, considering the people he has worked with, like Alex Ferguson at Manchester United and Terry Venables when he was at Barcelona.
"It's impossible to say whether anyone, great player or not, is going to be a successful manager but Mark has a great head start and as good a chance as anyone."
Hughes will need a coach to help him run day-to-day matters while he is still playing for Southampton, and an appointment could well be announced when the new manager names his first squad in a fortnight, for the Belarus game.
Names in the frame include Peter Shreeves, who was Terry Yorath's No 2. Ian Rush, Hughes' former strike partner, could also become involved.
It is, however, believed that Hughes will distance himself from the joint- caretaker manager role he undertook with Neville Southall for the Denmark game immediately after Gould's resignation.
The former Everton goalkeeper's future involvement in national team affairs is now unclear. Some senior players were said to be unimpressed with his bullish attitude before the Denmark match at Anfield.
Hughes was considered a safer option by the FAW, even if critics believe it has given control of the squad to the "millionaires' club", the name given to senior players like Hughes, Gary Speed, John Hartson, Ryan Giggs and Dean Saunders.