Charities believe investment management costs should be apportioned between business and non-business activities. VAT on investments that subsidise business activities can be reclaimed.
If HMRC agrees to follow a precedent set in a case involving the Children's Society in 2005 concerning VAT on fees paid to fundraisers, organisations will be able to reclaim a portion of the VAT paid on investment management fees for the past three years.
David Warrellow, tax manager at the National Trust and a member of the Charity Tax Group management committee, said HMRC had made several repayments to charities based on the method used for fundraisers, but had then stopped.
He said some organisations had been waiting 18 months to find out whether they would receive a rebate.
"HMRC seems embarrassed by how long it has taken, and has promised to make a quick response," he said.