Beginning this month, Yale will join the small number of United States colleges and universities that help offset a federal tax gay and lesbian employees pay on health coverage received by their partners.

Though same-sex marriage is legal in Connecticut, it is not recognized under federal law, so domestic partner health benefits are considered taxable income — levying an additional cost on homosexual couples that those in heterosexual marriages do not face. In a reversal from past years, Yale will now pay both employees with same-sex spouses or in civil unions $1,500 a year to help cover the cost of a federal tax on employer-provided health coverage for domestic partners, Compensation and Benefits Director Hugh Penney said in a Dec. 22 email.

“Because of the increasing discrepancies between the state and federal tax treatment of the health care benefits provided to same-sex marital partners, a number of employers have begun to partially or fully offset the federal tax,” Penney said. “Yale has long been progressive in providing equality of benefits for same-sex couples.”

The new policy brings Yale in line with Columbia University, Syracuse University and Bowdoin College — other schools that help offset the federal tax on domestic partner health coverage. Columbia also decided to implement the tax relief for 2012, and will provide annual reimbursements of $1,000, said Leif Mitchell, co-chair of Yale’s LGBTQ Affinity Group.

Mitchell said Saturday that the policy change came after months of discussion between administrators and members of the organization, which represents staff and faculty from across Yale.

Vice President for Human Resources and Administration Michael Peel and Penney presented the policy change to Yale’s officers in November, Mitchell said, along with a letter from the affinity group backing the proposal. He added that the group heard soon afterward that the administration had approved the reimbursement policy.

Under the new policy, employees will be reimbursed $125 each month if their partners are not offered coverage by their own employers and receive health benefits through the University instead, Mitchell said. In addition, only faculty or managerial and professional staff will be compensated because other University employees’ benefits must be negotiated through Yale’s unions, Mitchell said, making roughly 40 to 50 employees eligible.

Mitchell said he thinks $1,500 annually is an appropriate amount of compensation, as it will likely cover the entire amount of the federal tax for employees who have the University’s health plan. With more extensive insurance, Mitchell said it is possible the full amount of the tax would not be covered.

Administrators have also decided Yale will join the Human Rights Campaign’s Business Coalition for Benefits Tax Equity — a group of U.S. employers working to end the tax on health coverage for domestic partners, Mitchell said. The Human Rights Campaign is the nation’s largest organization in support of lesbian, gay, bisexual and transgender civil rights.

“Our LGBTQ employees made us aware of an inconsistency affecting their compensation,” Provost Peter Salovey said in a Saturday email. “We are pleased to join other progressive employers in addressing it.”

The University’s previous tax policy came under fire after Yale failed to withhold income that covered the federal tax on domestic partner health benefits in 2010 because of an accounting error. To correct the mistake, the University notified about 60 affected employees in December 2010 that it would deduct the funds from their 2011 salaries.

The University’s action prompted the Human Rights Campaign to ask that Yale pay for the 2010 mistake and offset the federal tax in the future.

The decision to make the 2012 change was not in response to the 2010 payroll problem, Penney said, but instead followed from discussions with LGBTQ employees that illustrated the “symbolic and financial importance” of the change. Mitchell said the Yale affinity group expressed its desire for the tax coverage at a January 2011 meeting with administrators and continued to discuss the issue throughout that year.

Same-sex marriage became legal in Connecticut in November 2008.