Figures from the British Trust for Ornithology (BTO) show that the rabbit population across the UK as a whole has fallen by around 60 per cent.
The Mammal Society, which is dedicated to the conservation of all mammals, now wants people to report sightings of the animals.
Professor Fiona Matthews, chair of the charity, described the BTO figures for Scotland as “worrying”.
She said: “In Scotland the declines look particularly large compared to the rest of the UK, and partly that might be because they are more on the edge of their range in much of Scotland.
“But we need to find out what’s going on because they are now such a fundamental part of our ecosystem.
“Things like stoats, rabbit is a major part of their diet; polecats use rabbit burrows and foxes prey on rabbits.
“If the rabbits aren’t there then you have all these other knock-on effects on everything else.”
Prof Matthews, professor of environmental biology at Sussex University, said that rabbits had been seen as a pest in the past and their existence taken for granted.
She said their decline could be due to a combination of persecution and diseases such as myxomatosis and the lesser-known rabbit haemorrhagic disease.
In Scotland, she said a lack of suitable habitat and weather – particularly snow in places – could also be factors.
She said: “Maybe rabbits are a bit like sparrows or bees. Until very recently these animals were just so common, we just assume they are everywhere – a bit of a nuisance almost.”
She added that there remained significant affection for the species, however, adding: “You just have to look at the popularity of Peter Rabbit – the rabbit has a dual role in our culture.
“On the one hand it’s the farmer’s enemy and ‘we must do everything we can to control it’, while on the other hand it has been here since Roman times, a lot of people have pet rabbits, children love them and they are an important part of our current ecosystem.”
The Mammal Society yesterday launched a new “Mammal Mapper App” to log sightings of mammals including rabbits.
The Mammal Society’s own estimate suggests that despite the fall in the population there may still be as many as ten to 15 million rabbits in Scotland.