The community infrastructure levy, which is contained in the Planning Bill, requires any organisation that gets planning permission to develop land to pay a tax based on the land's value.
New offices or business premises would be affected, along with village halls, churches, community groups and charities that are given consent to build extensions.
"This levy is intended as a tax on property developers' profits, but it will also hit charities," said Nick Ivey, head of property law at solicitors Bates Wells & Braithwaite. "The really unfair thing is that it will even hit charities that aren't planning on selling the land - just developing it for the good of the community.
"It seems a no-brainer that they should be exempted from this. Charities should not be fundraising to pay tax."
The Charity Tax Group, the Charities' Property Association, the Churches' Legislation Advisory Service and the NCVO have combined to fight for a charity exemption from the levy, which could become law next year.
The levy has been heavily criticised in the House of Lords. George Cassidy, Bishop of Southwell and Nottingham, said in a recent debate on the bill that churches and charities were very disturbed by the proposal.
"The levy will impose a new financial burden on them that they will find difficult to bear," he said.
"Schools and houses will not be built and the development of community facilities such as village halls will be hindered. Organisations that are already short of funds to care for important parts of the built heritage will have even less money for maintenance."
A Charity Tax Group spokesman said the levy would have a disastrous impact on charities' ability to develop their services. "Unlike commercial developers, charities will not be able to offset the cost of the tax against future profits," he said.