The EFL wrote to the club to "request their observations" on Wagner's team after their loss to Birmingham.
The Terriers boss made 10 changes for the 2-0 defeat, a result the league has confirmed will stand.
"The only person who is able to say what is a strong team and what isn't a strong team is me," Wagner said.
"I selected the team because I wanted to win the football match. In my opinion, and this is why I defend my squad and my players like a tiger, I think it's very disrespectful for the players who were on the grass against Birmingham to say this was a weak team.
"This is why I thought at the beginning it was a joke and not something serious."
Wagner's team selection was questioned by Blackburn boss Tony Mowbray, whose Rovers side remain two points below relegation rivals Birmingham before the final game of the season.
"It doesn't concern me to be fair what other managers from Nottingham or Birmingham or Blackburn or whoever thinks about us and our team selection," Wagner told BBC Radio Leeds.
"You have to be totally focused on yourself and you have to be brave enough if you make mistakes over the whole season - and I think if you are in relegation trouble after 45 games, probably you will not have done everything right - you have to be brave enough to raise your hand and say yes we did some mistakes.
"I don't think the team selection I chose against Birmingham will cause these teams problems over 46 games, this should not be the reason if someone is in trouble."
Huddersfield Town boss David Wagner says he thought it was a joke when the English Football League asked him to explain his team selection.