The Rainbow Tick initiative is defending itself, saying the ticks are not just marketing or window dressing.
Critics have questioned whether the certification was more than just a PR exercise and RNZ has revealed the case of a transgender woman who said she was bullied by a Fletcher Building manager - who was described as anti-LGBTQI.
Fletcher Building has had the Rainbow Tick since 2015.
All up, more than 70 organisations are registered with a tick.
Rainbow Tick programme manager Michael Stevens, said it was not a marketing exercise - it was about bringing change to an organisation.
"The data tells us that employees value it - they see benefit in it - that they see it offers them the opportunity to help bring about meaningful change within their organisations," he said.
Mr Stevens said it had never revoked an organisation's tick, however it had considered it on some occasions and won't rule it out in the future.
He said if employees of Rainbow Tick organisations had concerns about anti-LGBTQI behaviour, then they should come forward and speak up.
"If we had a group of LGBT employees sitting down with us going 'you know what this happened, this happened and this happened - and we don't think the company deserves a Rainbow Tick anymore' - we would take that very seriously," he said.