Unmarried same sex couples may owe the taxman £1,600, according to the Chartered Institute of Taxation (CIOT).
When gay and lesbian couples were granted civil partnership rights in 2005, the law also stated that even those couples who do not have a ceremony would be treated as a unit for tax credits.
Anne Redston of the Chartered Institute of Taxation said: “Previously same sex couples were treated as single people for the tax credit system. So two women who live together as a couple with one child each, would each have been treated as single parents.
“From 5 December onwards these couples’ tax credits may go down, perhaps by as much as £98 a week.”
The body claims warnings from HM Revenue and Customs were overlooked in the excitement of the new Civil Partnership rules.
Ms Redston said: “Same sex couples who are claiming tax credits should have told HMRC by now about their living arrangements. As each day passes their overpayment position could be getting worse. By now it could be as much as £1,600.”
Peter Tatchell, from gay group Outrage, said: “This is going to be a financial bombshell for thousands of same sex couples who have not entered into a civil partnership and therefore did not realise they would lose out financially.
“For some same sex couples on low incomes this could be a confirmable unexpected financial hardship.
“Outrage issued a warning about this problem last October, we urged the government to grant transitional protection but all our representations were dismissed, now thousands of same sex couples face the financial bombshell of having to repay benefits and tax.”