Any UK establishment other than a private home would have to pay £50 to register with the Environment Agency every three years.
It is not clear whether allotments will be charged.
The levy, which is set to raise thousands of pounds in extra revenue for the Government, has been condemned by opposition MPs as 'bizarre'.
But the Department of Environment, Food and Rural Affairs has put out new rules which would require businesses, schools and charities to register them every three years.
The new rules will also increase the number of places that are required to hold a waste permit, which costs £600.
The proposals have infuriated environmental campaigners who warn it would discourage people from disposing of household waste on compost heaps.
Tory environment spokesman Peter Ainsworth said: 'Penalising people for doing their bit for the environment is typical of the Government's confused and counter-productive approach.'
There are around 2553 sites in the UK which are currently registered as composting biodegradable waste.
Under the rule changes, 1685 - or 66 per cent of these - will in future require a permit at a cost of £600 each. The remainder will have to pay the £50 charge to register every three years. A Defra spokesman insisted the new rules were not yet finalised.
She added that under EU laws, organisations must have permits to carry out waste disposal. But smaller bodies can 'exempt' themselves from this by registering a compost heap.
My take: Registering my allotment compost heaps, you have to be joking! It also means that every public garden, plant nursery, and small grower will have to register. We are having to register for permission to do what we have been able to do freely for thousands of years. Now the town hall "jobsworths" will be able to order you to stop composting, if it takes their fancy.
Don't think that when, a few years later, they extend it to private homes you can just ignore the issue. Our masters have arial photographs of every building and piece of land in the UK, there will be no hiding from them. Probably, the ownership of a compost heap will be a feature of building taxes.