Football Association chief executive Mark Bullingham says Ivan Toney was not picked for England's World Cup squad on "footballing grounds".
Brentford striker Toney was charged with 232 alleged breaches of the FA's betting rules over a near-four-year period on Wednesday.
The 26-year-old has until next Thursday to respond after he previously stated he was cooperating with an investigation into any alleged infringements.
Toney, before the revelation of the ongoing investigation was announced, missed out on Gareth Southgate's 26-man squad for Qatar, though Bullingham insisted the decision was for on-field reasons.
"He was absolutely available for selection," Bullingham told the BBC. "He was not chosen on footballing grounds."
Newcastle United's Callum Wilson got the nod ahead of Toney, joining Harry Kane and Marcus Rashford as Southgate's striking options.
Toney is not the first English player to be charged for such alleged breaches, with Kieran Trippier – a member of England's squad – punished in December 2020.
Right-back Trippier, now of Newcastle, was handed a 10-week ban by the FA after giving out information for others to bet on his transfer from Tottenham to Atletico Madrid.
"I think our rules are very clear and we have had a small number of cases," Bullingham responded when asked if there was a problem within English football.
"Obviously, we will look to enforce the rules when they are broken."
England start their World Cup campaign against Iran on Monday, before facing the United States and Wales in Group B.