Pink Dot Hong Kong had been held annually from 2014, featuring a mixture of music performances, art and workshops promoting diversity and LGBTQ rights.
It drew nearly 7,000 participants two years ago but last year's event was cancelled because the festival was denied a venue "without explanation", according to organisers.
Pink Dot said their venue manager, real estate investor Link REIT, had told them this year that "due to licensing issues, the venue cannot be rented", even as the carnival was making its final preparations.
It comes as another setback to the city's LGBTQ community after Hong Kong's legislature overwhelmingly voted down a bill in September that would have granted limited rights to same-sex couples.
"Faced with (venue) uncertainty, given the tight timeline and the involvement of numerous partner organizations... we have had to make the difficult decision to cancel" the June event, Pink Dot said.
"With just one month to go until the scheduled event date, we have been diligently following procedures to apply for the necessary licences but have not yet received approval from the relevant authorities," the organisers said.
Link REIT said when asked for comment that it had been liaising with the organisers "to support the event's preparation".
"In line with standard requirements, the use of the venue is subject to the organiser obtaining all licences required under applicable laws," it said in a statement.
The West Kowloon Cultural District, a statutory body whose members are appointed by the government, denied Pink Dot a venue last year "without explanation", organisers said at the time.