"We were expecting it but we can't do anything about it unfortunately," said Johnson.
"It is the little clubs that suffer and I don't think it should happen but FIFA decides these things.
"The games have to be some time but it would be much better if they are midweek when we haven't got games.
"The smaller clubs are more likely to have Wales, Scotland or Ireland Under-21s players.
"And it's not always good for the player because if they are away they might not get their place back."
Defender James Wilson and winger Dean Grubb are on standby for the Wales Under-21s while Wilson and full-back Christian Ribeiro are in the Wales Under-19s squad with another academy prospect, striker Josh Klein-Davis, on standby.