The alleged breaches took place between 25 February 2017 and 23 January 2021.
Toney, 26, has scored 10 Premier League goals this season but missed out on a place in the England World Cup squad.
Brentford said in a statement: “The club has been in discussion with Ivan and his legal representatives. Those conversations will continue privately.”
The statement continued: “We will make no further comment until the matter has been completed.”
He said earlier this month, after the allegations were first reported, that he was “assisting the Football Association with their enquiries”.
He was on the books at Newcastle United from 2015-2018 but spent the majority of that time out on loan. The Northampton-born player had two spells at Scunthorpe United, playing for them in the 2016-17 season and again from January to May 2018, either side of six months on loan at Wigan.
He has scored 58 goals in 105 appearances for Brentford, including two in a shock 2-1 win at defending Premier League champions Manchester City in the final game before the World Cup break.
Only England captain Harry Kane (12) and City forward Erling Haaland (18) have scored more goals in the Premier League this season.
Toney received his first England call-up for September’s Nations League games against Italy and Germany but did not get on the pitch in either.