US Ambassador Samantha Power said the NGOs taken off the list of participants "appear to have been chosen for their involvement in LGBTI, transgender or youth advocacy."
In a letter to UN General Assembly president Mogens Lykketoft, Power requested that these groups, including the US-based Global Action for Trans Equality, be allowed to take part in the June 8-10 high-level meeting on HIV/AIDS.
European Union Ambassador Joao Vale de Almeida said the NGOs had been struck from the list following objections from member states and requested information on which countries opposed their presence.
The EU ambassador wrote in his letter sent last week that changes to an initial list of delegations were made without consulting member states.
"Given that transgender people are 49 times more likely to be living with HIV than the general population, their exclusion from the high-level meeting will only impede global progress in combatting the HIV/AIDS pandemic and achieving the goal of an AIDS-free generation," Power wrote in her letter.