SCOT-PEP said unannounced "welfare visits" on sex workers who work from home were being brought in by police as part of Operation Lingle.
The charity, which promotes sex workers' rights, health and dignity, raised fears over "surprise police visits", which are to be piloted in Glasgow.
It branded them a "draconian shift in policy" and claimed where sex workers work alone, they could be intimidated.
The charity is concerned about possible risks to safety, arguing as it is a crime for sex workers to work together they could fear arrest after a welfare visit and could instead choose to work by themselves.
Members of the public will be encouraged to report neighbours to the police if they think they are operating as sex workers as part of the operation, SCOT-PEP claimed.
It is demanding a meeting with the Scottish Government, while Green MSP Patrick Harvie is to table questions on the issue at Holyrood in a bid to uncover what discussions ministers have had with Police Scotland about Operation Lingle, "which seeks to target indoor sex workers in Glasgow for what are described as 'unannounced welfare visits'".
The Glasgow MSP said: "If home visits are supposed to be about welfare, they should be delivered by an agency with a clear harm reduction ethos, not by the police after soliciting tip-offs from people's neighbours.
"Scotland has a very poor track record of harm reduction in this area, and I would urge the Scottish Government and Police Scotland to reconsider this operation urgently. Our priority should be protecting sex workers against violence and exploitation, not intimidating them and using police intelligence to identify and harass them."
A poll by Survation in May found that 86.8% of Scots supported changing the law to make it legal for two or more sex workers to work independently from the same property, with 13.2% opposed.
One sex worker, only identified as Cat, said: "I work with a friend because it's so much safer. If a client were to turn nasty, I'd know I have her in the other room to help. Unbelievably though, working together means we could both get arrested.
"This operation makes me think I should start working alone, which is so so scary. There's so many assaults on women in Glasgow."
Selling and purchasing sex is legal in Scotland unless it is solicited in public or done through a brothel or pimp
A sex worker called Amy said: "The idea that I could open the door to an unexpected visit from the police is really frightening. This is about making us feel hunted, like criminals, even when we're not breaking any laws."
A SCOT-PEP board member said: "No other members of the public are ever exposed to surprise police visits simply because of the nature of the lawful work they do. This scheme singles out sex workers for persecution and intimidation."
They added: "What's not clear, however, is whether Scottish ministers have approved this draconian shift in policy or whether Police Scotland are acting on their own initiative here.
"We are therefore grateful to Patrick Harvie MSP for lodging a series of parliamentary questions today to establish the basis for this potentially highly damaging new approach, which we believe could seriously undermine community relations and drive sex workers further underground.
"We will today also request an urgent meeting with Kenny MacAskill, the Cabinet Secretary for Justice, and we will be asking him to put this operation on hold until it can be given proper public scrutiny, and ideally either scrapped altogether or replaced by a policy which puts the safety of sex workers ahead of some counterproductive sense of moral panic.
"The evidence is clear - the public want to see the laws changed to protect sex workers, not the imposition of this sort of punitive 'raids in disguise'."
Detective Chief Inspector Ruth Gilfillan, of the National Rape Taskforce and Human Trafficking Unit, insisted the operation is not about criminalising sex workers
She has been involved in the development of Operation Lingle, a pilot initiative proposed for Glasgow, and said: "Police Scotland and a wide range of partners, including the local authority, health and third sector organisations, including SCOT-PEP, want to improve the safety, improve engagement and address the support needs of those working in the off-street sex industry."
Ms Gilfillan added it was anticipated the operation would improve the safety of sex workers and build trust in the police, as well as identifying those at risk and helping them get support.
"This is categorically not about criminalising sex workers and it's factually inaccurate to claim otherwise," she said.
"The visits would involve a support worker with a police officer and the main aim is to improve welfare and build trust. The whole concept is built around consultation with partners about the feasibility of the approach and the consent of the individuals being visited."
She added: "It was established that there was little documented information on the scale, threat, risk and harm to those working in the off-street industry. The proposed operation is one of the ways in which partners wanted to address that.
"Police Scotland remains committed to keeping people safe. It is recognised that prostitution is a sensitive and complex issue. That's the reason why a wide range of views were sought. It is disappointing that the aims and objectives of the multi-agency approach appear to have been misinterpreted. Police Scotland remains committed to working with all of our partners including SCOT-PEP."
A Scottish Government spokeswoman said: "These are operational matters for Police Scotland. We will consider SCOT-PEP's request for a meeting with the Cabinet Secretary, once a formal request has been received."