MK Dons boss Karl Robinson will talk to the Football Association about the use of teenager Dele Alli.
The 18-year-old featured for the England Under-19s on Wednesday, three days before MK face Leyton Orient in League One.
"I'm not happy about that. That will be something I'll be bringing up," Robinson told BBC Three Counties Radio.
"Dele is unique as he plays every week. I may have to rest him on Saturday, which is hard for fans to accept."
Despite his tender age, Alli is a key player for Robinson's League One side, who are currently fourth in the table and chasing promotion.
Alli has scored six goals in 13 games from midfield this season and is expected to join a Premier League club within the next 12 months.
He featured in two of England Under-19s' three European regional qualifiers in Greece this week.
"I understand we have a duty of care for the development of young players," Robinson said.
"In the eyes of the FA they have looked after Dele, because they rested him on Sunday and he's only played in two of the three games.
"From a welfare and physical perspective, they've probably done right.
"But they know that he is probably the only one in that team who is playing on Saturday. There are teething problems because this is an elite player."
Liverpool's Raheem Sterling has been in the middle of a similar dispute between club and country this week, after the 19-year-old said he was too tired to start the 1-0 European Championship qualifier win in Estonia.