The comments have been widely criticised by survivors groups and political opponents who said they downplayed the seriousness and lasting trauma of rape.
The SCRA, which comprises support groups in Glasgow, Lanarkshire, Ayrshire and the Western Isles, said the impacts of rape can last a lifetime, and the crime should never be reduced to a theoretical debate.
In an open letter the alliance said: "We are not demonising rape. We are naming it."
The authors strongly opposed the idea of rape existing on a "spectrum", insisting "there is no hierarchy of rape" and that no survivor should feel compelled to ask whether their experience was serious enough."
The letter urged politicians "not to normalise" rape or sexual violence, and "not create hierarchies of harm".
While not naming Manivannan, the United Nations Special Rapporteur on Violence against Women and Girls, Reem Alsalem, posted on X that rape should never be spoken about in terms of it being a spectrum.
Scotland's Children's Minister Siobhan Brown told the BBC's Sunday Show Manivannan's words were misjudged.
Scottish Labour and the Scottish Liberal Democrats have also been critical, while the Scottish Conservatives called on the Scottish Greens to suspend the MSP.
Meghan Gallacher, the party's equalities spokeswoman, said: "It is deeply alarming that anyone, but especially an elected representative, would ever seek to minimise the seriousness of rape and suggest that there is a spectrum of offences."
In a statement issued on Monday afternoon, Manivannan said they were "horrified" that the comments had been "selectively edited in order to mislead people and misrepresent me".
"I also accept that my language was abstract in the first place and for that I take full responsibility and am sorry," they said.
The MSP said that during the interview they had categorically stated that every rape in every context is equally serious and harmful but this had been "maliciously" left out of clips.
They added: "I recognise that the words in the clip shared, without the full context of the conversation, have caused considerable upset.
"For that I apologise. I will always stand with and for victims and survivors."
Manivannan said they were themselves a survivor of sexual violence and understood the enduring trauma of such an experience.
"I would never seek to diminish or dismiss any survivor's experience, or to make anyone feel that their pain was not heard or understood," they added.
"I am genuinely sorry to everyone who has been distressed, hurt or triggered by the clips, and by the discussion and coverage that has followed.
"Words matter, particularly when speaking about something as deeply personal and painful as sexual violence, and I regret this hurt caused."
Manivannan, who was elected as a list MSP representing Edinburgh and Lothians East under Scotland's proportional representation system, said they would welcome the opportunity to meet survivor and advocacy groups to listen to their perspectives.
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