HM Revenue & Customs gave charities immunity from the Construction Industry Scheme, introduced last year to ensure construction companies paid their taxes on time.
But Justine Riccomini, CIS expert at accountancy firm Scott-Moncrieff, told Third Sector that organisations such as housing associations could still be affected if they have trading subsidiaries involved in construction.
Riccomini warned that charities affected by the scheme should file monthly accounts and could face a fine for each month they do not pay for up to six years. She added that HMRC will not accept ignorance of the law as an excuse.
"If HMRC believes a subsidiary of a charitable body is failing to comply, and carries out an inspection, it may come down hard," she said.