Minimum wage rules say that if a charity pays anything over and above normal expenses to a volunteer, they are deemed to have a contract with that person, which would entitle her or him to claim the minimum wage.
The department has decided that childcare costs should be considered a benefit rather than an expense.
In its consultation on volunteers and the minimum wage, Berr said that reimbursing childcare costs would "represent a significant benefit in kind and as such would change the nature of the relationship between voluntary worker and qualifying organisation".
However, the Association of Volunteer Managers has launched a campaign to reverse the decision.
It said it feared that if voluntary organisations were to stop reimbursing childcare costs, it would deter carers on low incomes from volunteering.
It argued that Berr's line contradicted guidelines from the Department for Work and Pensions and legal precedent.
In the 2004 case of South East Sheffield Citizens Advice Bureau v Grayson, the provision of childcare expenses and other out-of-pocket expenses was considered reasonable and did not amount to a benefit to volunteers.
"It's another example of government departments not communicating with each other," said Kate Bowgett, a member of the Association of Volunteer Managers. "We don't believe Berr has a legal leg to stand on, and this definitely isn't in line with Gordon Brown's drive to boost volunteer numbers.
"More and more organisations are reimbursing costs for volunteers who are carers, so it would be very sad if they had to stop doing it."
The association is now calling on volunteer managers to write to Berr in protest.
A spokeswoman for Berr said: "The Government response to consultation said there was concern over whether the provision of childcare or reimbursement of childcare expenses could alter the nature of volunteering by introducing an element of obligation or gain.
"We have noted the issues raised on this post-consultation, and will continue to work with voluntary organisations on this issue."
Last year, the DWP reversed its decision that volunteers would forfeit income support or jobseeker's allowance if they claimed lunch expenses from the charity.
This decision was made after a three-month dispute with charities (Third Sector, 11 October 2006).