Professional Game Match Officials Limited (PGMOL) believe the programme 'Britain's Gay Footballers', which is due to be shown on BBC Three next Monday, effectively accuses them of gagging the official.
PGMOL have said they are writing to producers and the BBC urging them to correct a number of "factual errors" before the documentary is aired.
PGMOL, which oversees refereeing in the professional game, do not allow officials to speak to the media on any subject - aside, occasionally, from matters of officiating - during the season.
They say it is for this reason alone that the official cannot speak and any other issues are irrelevant. Interview requests are regularly turned down as a matter of policy.
There are some other aspects of this section of the programme the body are unhappy with.
A spokesperson for PGMOL said: "There are a number of alarming factual errors and we are writing to the programme-makers and the BBC to ensure these are addressed."
The BBC did not want to comment fully until receiving the letter.
The programme is hosted by Amal Fashanu, niece of the late Justin Fashanu, who in 1990 became the first, and so far only, professional British footballer to come out as gay.