The National LGBTI Health Alliance has raised several concerns in a submission to a Senate inquiry into airport and aviation security.

The submission detailed the experience of one anonymous person whose prosthetic was detected in their underwear while they underwent a body scan.

The situation created a chain of events that ended with officers forcing the person to remove it and place it in a tray.

The officers allegedly made a spectacle of the person before putting on gloves and repeatedly referring to the prosthetic as "that thing".

That person relayed their story to the National LGBI Alliance to be included in the submission.

The person was taken into what they said was a small room with two men.

"I pulled out my prosthetic enough for them to see," they said in the submission.

"The supervisor said I needed to sign a form first and, while saying this, he put on a second glove.

"I asked him again what the gloves were for and he replied, 'you want me to touch that thing with my bare hands?'

"After I signed the document I removed my prosthetic and placed it in a tray."

'Public spectacle for his own amusement'

The person said the supervisor had no regard for them as a human being.

"Firstly, I was made a public spectacle of for his own amusement," they said.

"Secondly, his actions and words trivialised the importance that this prosthetic was to me by referring to it as 'that thing'.

"Thirdly, glaring at me by the doorway while I replaced my prosthetic after that search, it left me feeling humiliated and degraded."

Another anonymous person's story was included in the submission after they say they were discriminated against when the scanner went over their chest.

"On one occasion, when scanned using the new body scanners, the device showed up an issue in the breast/chest region, which it wouldn't have done if it wasn't set to treat men differently to women," they said in the submission.

Transgender woman 'laughed at' after being called 'sir'

Another was allegedly called "sir", before saying she was a woman, only to hear officers laugh as she walked away.

"I was called 'sir' by one of two security people in a Melbourne domestic terminal," she said in the submission.

"I politely pointed out I was female and they corrected how I was addressed for the rest of my interaction.

"However, as I walked away, I heard them laughing derisively.

"I find it extremely concerning that people in a position of such responsibility effectively lied to my face."

Airport protocols in breach of Sex Discrimination Act: Alliance

The submission also raises concerns about a lack of recognition and inclusion of people with so called "X" sex marker on their passports.

Rebecca Reynolds is the executive director of the National LGBTI Health Alliance and she said airport protocols appear to be in breach of the Sex Discrimination Act.

"We are deeply concerned that the electronic booking systems, security protocols, and other aspects of standard operating procedure of the major commercial aviation carriers in Australia appear to be in breach of the Sex Discrimination Act 1984 with regard to gender identity and intersex status," she told the ABC.

"We have also heard reports of sexual orientation and relationship status discrimination that appear to violate this legislation."

She said some LGBTI people opt out of flying due to fears of discrimination.

"Basically, members are avoiding air travel, feeling marginalised and socially excluded, hindered in the performance of their employment that involves travel, or experiencing anxiety and adverse mental health effects as a result of this discrimination," she said.

Ms Reynolds said new measures need to be developed to end what she calls "the climate of pervasive discrimination against LGBTI populations during security checks".

"A better approach would be to work with the Alliance to change existing policies, databases, and security screening protocols and to ensure that all staff receive ongoing training to comply with federal anti-discrimination legislation," she said.

"In addition, airlines must ensure that third party contractors, such as security personnel and other airlines with whom they engage in code-sharing, are equally consistent in complying with federal anti-discrimination legislation."