Speaking to The Scotsman at his party’s annual conference, he insisted the LGBT+ community was “overwhelmingly united” in favour of trans rights.
His comments were in reaction to reports that the BBC is expected to quit Stonewall’s diversity champions programme.
The LGBT+ charity states the programme is “the leading employers’ programme for ensuring all LGBT+ staff are accepted without exception in the workplace” and has around 800 public and private business members.
However, the decision from the BBC to leave the scheme follows a similar decision by the media regulator Ofcom, the Equality and Human Rights Commission, and the UK Government’s Cabinet Office.
Scottish politics has been deeply divided by an increasing fraught and bitter debate around self-identification for transgender people and the reform of the Gender Recognition Act.
The Scottish Greens were also hit by controversy after Andy Wightman, one of the party’s most high profile MSPs, quit due to the party’s “alienating and provocative” stance on trans rights.
Mr Harvie said it would be “extremely disappointing” if the reports the BBC is set to leave Stonewall’s scheme were true.
He said: “Stonewall is the biggest and successful LGBT+ human rights organisation in Europe, it has done incredibly work, it still does incredible work.
"Now it is under fundamental attack by those who have never supported my community’s human rights, who are mobilising around an opportunistic hate campaign specifically targeted against trans and non-binary people at the moment.
"It’s disgraceful, that hate campaign, it is really really prominent across the media and across all too much of politics as well.”
Mr Harvie and fellow co-leader Lorna Slater were appointed government ministers as part of the cooperation agreement between the SNP and the Scottish Greens, which included a commitment to advance reforms to the Gender Recognition Act.
The Glasgow MSP said that he was “really pleased” movement on this would take place during this session of parliament .
"We will not allow ourselves to fragmented in a way that some would like because we know where that will go,” he said.
"That will go toward where Texas is at the moment with fundamental attacks, not just on queer people’s human rights but on women’s reproductive rights as well.
"Promises that have been delayed for far too long will now be delivered as well as improvements on trans people’s health care.”
Responding, a spokesperson for the BBC said it acts independently in all aspects of its operations and has its own values and editorial standards.
They added: “We aim to be industry leading on workforce inclusion and take advice from a range of external organisations, however we make the final decision on any BBC policies or practices ourselves. We do not take legal advice from Stonewall and we do not subscribe to Stonewall’s campaigning.
"The charity simply provides advice that we are able to consider.”