The helpline is for those who have lost their jobs or feel they are threatened because of their sexuality and need to talk in confidence.
Navy News, an award-winning journal run by civil servants, declined to accept an advert promoting the number for fear of security risks.
Rank Outsiders, a support and lobby group which campaigns for the lifting of the ban on lesbians and gay men in the military, was thwarted 18 months ago in an attempt to promote its helpline in all three service newspapers, but felt confident Navy News would take the advert this time.
The group's spokesman, Lieutenant Commander Patrick Lyster-Todd, said the decision was made for reasons which "are amongst the more irrational and easily challenged that I have yet to encounter.
"It's very disappointing and we do feel annoyed. It's a skirmish lost," he said.
He accused the Ministry of Defence of backtracking: "In the past the MoD has said they reckoned this number was a useful service and yet this newspaper, for reasons which can be blown away in one breath, won't let us reach out to the people for whom we exist. The real reason is that they don't want to deal with the fact that they might get criticism for running it."
The editor of Navy News, Jim Allaway, said he made the decision not to take the advert for fear that confidential records of military personnel might fall into the wrong hands.
"The feeling is that we would be reluctant to do something at this stage because of the pressure of blackmail," he said.
"It's still an offence within the Navy which could result in dismissal. If a person was discovered, he could be an easy target."Reuse content