Carl Everall, who has been coaching in the academy since 2013, has been suspended by the club and the FA pending the inquiries into allegations over his behaviour.
“This is a safeguarding and police matter so therefore the FA is not in a position to comment,” an FA spokesman said.
Before working with Crewe, Everall was a coach at Port Vale, and up until 14 months ago he was joint manager at Whitchurch Alport. He then moved to work full-time for the 'Railwaymen'.
The news comes not long after a hugely damaging investigation into former coach Barry Bennell - amongst others - who was imprisoned for 30 years for abusing youth players at the club. So far, at least 97 players have come forward with allegations.
“You will appreciate that it is not appropriate for us to comment in detail at this time,” chairman John Bowler said in a statement. “I can, however, confirm that all relevant and appropriate procedures have been followed."
Director of football, Dario Gradi, who employed Bennell at Crewe, has been suspended from from since 2016. He has a 35-year history with the club in various roles including manager.