The group's State of Nature 2016 report says 18% of butterflies, 15% of dragonflies and 13% of plants face dying out.
Across the UK, 13% of species assessed are under threat of disappearing.
The report calls for "significant investment in the environment to ensure year-on-year improvement".
It says changes in agricultural practices - including the use of pesticides and the loss of hedgerows - are among the biggest factors behind the "widespread decline" of nature.
The State of Nature 2016 UK report will be launched by Sir David Attenborough in London on Wednesday.
It will be followed later by separate launches in Edinburgh, Belfast and Cardiff.
Sir David said: "The natural world is in serious trouble and it needs our help as never before.
"The rallying call issued after the State of Nature report in 2013 has promoted exciting and innovative conservation projects. Landscapes are being restored, special places defended, struggling species being saved and brought back.
"But we need to build significantly on this progress if we are to provide a bright future for nature and for people. The future of nature is under threat and we must work together; governments, conservationists, businesses and individuals, to help it."
The Edinburgh event will be held at the Holyrood Hotel and will be attended by Environment Secretary Roseanna Cunningham, as well as leading conservation and research organisations.
Ms Cunningham said: "This report highlights the challenges which lie ahead in conserving Scotland's wonderful nature.
"The Scottish government is committed to driving forward Scotland's Biodiversity Strategy, the 2020 Challenge for Scotland's Biodiversity, and its accompanying Route Map to 2020.
"We will publish a progress report at the end of this month and early indications show the majority of actions included in the Route Map are on track to achieve their targets.
"We have so much to be proud of in Scotland and so much to protect and enhance. That means we all have much work to do and I look forward to working with our partners to improve the state of nature in Scotland."
Mark Eaton, one of the lead authors on the report, said "ambitious action" was needed to preserve Scotland's natural world.
He said: "Never before have we known this much about the state of nature in Scotland and the threats it is facing.
"The partnership and many landowners are using the knowledge we're gathering to underpin some amazing scientific and conservation work. But more is needed to put nature back where it belongs - we must continue to work to help restore our land and sea for wildlife.
"There is a real opportunity for the Scottish and UK governments to build on these efforts and deliver the significant investment and ambitious action needed to bring nature back from the brink."

Michael Birch, 44, was one of 23 people injured in the accident in East Mersea near Colchester, on 23 September.
His wife Gemma has told the BBC her husband was "very lucky to be alive".
Six people involved in the crash were taken to hospital with serious injuries. Essex Police would not reveal their current condition.
Mr Birch has so far had four operations and his wife said it was "too early" to say if he would fully recover, but he was making "good progress".
He is still being treated at the Royal London Hospital for injuries sustained after being crushed by the steam engine.
Mrs Birch described the moment she first saw him with "pipes and tubes everywhere, it was just horrible".
She was told he was "really, really poorly" but doctors were "doing all they could".
Two weeks after the crash, she said her husband was "making good progress". "They're happy with him at the minute."
Mr Birch has undergone four procedures to repair his bowel, take fragments of glass out of his body and has had reconstructive surgery on his hand.
He is conscious but "very tired - just taking each day as it comes", his wife said.
He had not really spoken about his injuries, she said, although he was aware of the extent of them.
"I don't think he's ready," she added.
Asked if her husband would be able to return to his job as a bus driver, she said: "I don't know that.
"He's quite a determined person so we'll just have to wait and see.
"It's been hard, but we're getting there."
A fundraising page set up to help Mr Birch's family has so far raised more than Â£1,200.
A 51-year-old Great Yarmouth man arrested after the collision on suspicion of causing serious injury by dangerous driving was released on police bail.
One in 11 native species of animals and plants in Scotland is at risk of extinction, a report by 50 wildlife and research organisations has suggested.
[NEXT_CONCEPT]
A bus driver who was seriously hurt when a steam engine fell off a lorry into the path of his vehicle remains "really poorly", his wife has said.