His Foundation for Integrated Health charity says without regulation new EU laws will ban most of the trade, forcing patients to use bogus outlets.
From 2011 EU legislation will permit only statutorily registered professionals like doctors to prescribe manufactured herbal remedies.
The government says it will reach a decision in the new year.
Britons spend about £1.6?billion a year on alternative remedies.
There is currently no official system of regulation in the UK, meaning anyone can treat.
But there are codes under which practitioners use remedies manufactured to recognisable standards.
The EU Directive that will be implemented from April 2011 will restrict herbal medicines that can be supplied over-the-counter to licensed "traditional" medicines used to treat "mild and self-limiting" conditions - basically meaning nothing worse than a cold.
At the same time, it will become unlawful for anyone except "statutorily regulated" professionals to treat patients with any other herbal medicines, except those that a herbalist prepares personally on his/her own premises.
The Prince's Foundation says this will mean many herbalists will no longer be able to offer remedies to their clients and patients will instead turn to the black market.
There have been cases where people have died because the remedies they have bought from dubious sources have contained unsafe ingredients, such as arsenic or lead.
The Foundation believes regulation would resolve this, by bringing vetted herbalists within the EU law.
But this is at odds with eminent scientists who sceptical about herbalism and are against statutory regulation on the grounds it would make such treatments "respectable".
Professor George Lewith, a doctor and expert in complementary medicine, said: "Failing to introduce statutory regulation will amount to a Quack's Charter.
"It is the incompetent and the irresponsible we need to stop. Not the well-trained, dedicated herbalists who put their patients first.
"We cannot wash our hands of responsibility for herbal medicine and the patients who use it.
"No-one deserves to die for no better reason than preferring herbal remedies to conventional medicine."
Professor David Colquhoun, an expert in pharmacology at University College London, said the Prince's suggestions were wrong and would not safeguard patients.
"We do need regulation, but not the sort of ineffective regulation the Prince wants. Proper regulation should be on whether these products work.
"The rules should be the same as for all drugs."
A spokeswoman from the UK charity Sense About Science said: "The professional regulation proposed by the Government and supported by the Foundation for Integrated Health for herbal medicine practitioners, and which doesn't include any requirement for evidence of efficacy, imitates the regulation of science-based medical practice.
"It suggests to the public that these practices are part of, or equivalent to, science-based medical practice when they have none of the content of science-based medical practice."