The Scottish Society for the Prevention of Cruelty to Animals is trying to establish whether there is a link with black magic.
The incidents have ranged from sexual abuse and slashings to "odd" behaviour such as the plaiting of horses' manes.
Research carried out by the National Equine Welfare Council suggested that there may be a link with an ancient black magic calendar.
However, SSPCA spokeswoman Doreen Graham told BBC Scotland that she had made a "faux pas" by describing this as a pagan calendar.
"That was an error on my part and I would like them to accept my unreserved apology," she said.
"What we are talking about is people involved in the dark side.
"The pagan community has been very supportive. They are very at one with nature and they are actually trying to help with our investigation."
'Vile act'
She said the SSPCA would be meeting regularly with the head of the pagan community, who was trying to help identify some of the dates of attacks.
The pagan community has already denied any involvement with the incidents.
The president of the Glasgow University Pagan Society wrote to BBC News Online saying that pagans were "appalled" to have been implicated in such a "vile act".
"We do not harm animals or human beings. On the contrary, we feel it is our duty to protect this planet and all the creatures that we share it with."
Ms Graham told BBC Scotland that the attacks on horses took a number of different forms, including the cutting of tails.
"We have also had sexual abuse of horses and horses being very badly slashed. These are cases of cruelty that we would investigate," she said.
"But there have been other instances that we would like people to let us know about.
"People may now find that their horse's mane has been plaited with a sticky substance and there may be odd things in the field, there may be odd symbols."
'Cover of darkness'
The SSPCA wants to hear about any such incidents so they can be logged.
The results of the Scottish research will combined with similar studies being carried out in England and Wales to see if there is a pattern.
"It may be that people who want to carry out these acts against horses are using the cover of darkness," added Ms Graham.
"It could be as simple as that, but if we can link it in with anything else it could be helpful."
Hair removed
She added that the International League for the Protection of Horses had tips on improving horse security on its website, including the creation of horsewatch groups.
In recent weeks horses have been attacked near Coupar Angus, north west of Dundee, and in filed around Aberdeen.
Owner Jackie Boyd, whose horses had hair removed from their tails on the outskirts of Aberdeen, said she was "horrified" by suggestions of a link to witchcraft.
Further information is available from the Scottish SPCA on 0131 338 5605 or from the National Equine Welfare Council on: 01295 810060.