Prisoners who have consensual sex while inside jail face being separated and possibly disciplined, prison governors have told the first review of sex behind bars in England and Wales.

Prisoners have told an independent commission that the policy of separating prisoners believed to be in a sexual relationship was discriminatory towards openly gay prisoners.

Sexual health charities, including the National Aids Trust, have also warned that attempts to control consensual sexual activity between prisoners risk undermining efforts to promote safe sex and prevent the spread of HIV, such as access to condoms.

The commission on sex in prison, set up by the Howard League for Penal Reform, is made up of academics, former prison governors, health experts, a former prisons minister and a former solicitor-general.

It says in its first briefing paper that although it is clear that some male prisoners are having sex, there has been little research on consensual activity and little reliable data.

The British Association for Sexual Health and HIV told the commission that evidence of sex in prison was largely anecdotal but widely reported in male and female prisons.

But while female prisoners were quite open with clinical staff about sex with other prisoners, this was not the same in male jails where denial of sexual activity was more common. "This may be because male prisoners perceived there was more of a stigma attached to men who have sex with men," says the commission's briefing paper.

The Terence Higgins Trust said that prison officers believed prisoners did have sex but that it was rare for people to be found engaging in sex. The trust said the fact that homophobic attitudes were more pronounced among young men inside jails than in the community could account for the reluctance of male prisoners to admit to sex with other men.

Sexual health workers used the term "heteroflexible" to describe men who identify themselves as heterosexual but are flexible about having sex with men while they are in prison. Prisoners serving longer sentences were more likely to acknowledge a gay identity. Although there is no prison rule banning sex between prisoners, prison staff do not allow prisoners to have sex. Prison governors say it is difficult, if not impossible, for prison staff to be able to distinguish between consensual and coercive sexual relationships between prisoners.

One gay prisoner told the commissioners: "In the four prisons I have been held at, I have never been aware of any prisoner being charged for having consensual sex with a cell mate. I have however witnessed openly gay partners being split up and moved to other wings, simply because they were 'together', although no sexual activity had taken place."

Another inmate reported: "Officers would push open my door very quickly, unannounced, in an attempt to catch us having sex. Of course it never worked but it put us on edge all the time. A senior officer did this once as Simon and I were sat on my bed holding hands watching a movie on TV. He ordered us to stop holding hands and move apart, or he would give us an IEP [incentives and earned privileges] warning."

Prisoners who did not want officers to know they were having sex told the commission that they were often unable to obtain condoms in confidence. The chief inspector of prisons has reported that in some jails barrier protection, dental dams, lubricants and confidential advice are all widely available while in others condoms were only available if the prisoner attended a clinic.

Chris Sheffield, a former prison governor who chairs the commission, said: "Prisons need to ensure that they protect the vulnerable. The prison population is a high-risk group for sexually transmitted infections and risk-taking sexual behaviour.

"The need for harm reduction measures and the delivery of sexual health policies are important not just for prisoners but wider society."

A prison service spokeswoman said: "Sexual relations between prisoners are not commonplace. We do not condone sex in prisons or believe that prisoners in a relationship should share a cell. Reported incidents of sexual assault in prison are rare."

She said that where a sexual assault was reported or discovered, it would be investigated and reported to the police as necessary.