Albion's football coaching scheme for schools and youth groups has been told not to discriminate against women to be successful in grant applications.
The Football in the Community scheme lost out on a £5,000 grant in the latest round of handouts by Brighton and Hove City Council.
The council says the reason the grant was not given had nothing to do with the apparent discrepancy in charges for men and boys and women and girls.
But it has told the club to ensure the charges are in line for future applications.
Albion chief executive Martin Perry said the only times people were charged differently was for different courses.
The club is among dozens of groups which have lost money after the council altered the way it awards cash to charities and community.
The ten-year-old scheme teaches football skills, mostly to young people at schools and youth groups.
Mr Perry said the scheme would be hit by the council's decision to stop the annual grant but it would not have to shut down.
He said: "We are exceedingly disappointed and feel it is an extremely poor decision."
A council spokeswoman confirmed the club had been asked to bring its charges for women and girls into line with those for men and boys, or to prove they already were in line.
"On paper, that does not seem to be the case. This was not the reason for the grant decision, it was a comment relating to future applications.
"We would like Brighton and Hove Albion to provide us with data on the subscriptions to the many teams they run."
There has been anger at the way money in the council's grants programme was allocated.
The Citizens' Advice Bureau office in Hove might have to shut after its grant was cut by £67,000. Among other groups hit were the Hangleton and Knoll Project and the Money Advice and Community Support Service.
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