Though a recent survey of universities reported more schools than ever now offer the same healthcare and benefits to same-sex partners of employees in civil unions and marriages, some schools in Massachusetts — the only state to legalize gay marriage — are using federal laws to deny gay couples equal benefits.

According to the survey conducted this year by the College and University Professional Association for Human Resources, 40 percent of colleges offer healthcare coverage to employees in same-sex marriages and legal unions, an increase from last year’s 38 percent.

Massachusetts schools have been legally obligated to offer the same healthcare coverage and benefits to spouses of all married employees regardless of sexuality since 2004, when the State Supreme Judicial Court legalized same-sex marriage. But some schools have found loopholes to avoid covering certain costs.

Boston College, a Roman Catholic school, provides the same benefits to all married couples but makes gay married couples pay their own federal taxes, said BC benefits specialist Anabelle Murphy.

“We are recognizing the new law that recognizes same-sex marriages,” Murphy said. “The only difference is that we tax the employee.”

Murphy said the university covers federal taxes placed on health benefits for straight married couples but requires gay couples to pay their own federal taxes based on the Defense of Marriage Act, which was passed in 1996. The act gives states that prohibit same-sex marriage the right to disregard same-sex marriage contracts from other states and denies federal recognition of same-sex marriages.

On its website, the BC benefits office includes a separate section describing tax information for healthcare provided to spouses in same-sex marriages.

According to the Department of Human Resources at the University of Massachusetts, the school offers all married couples the same benefits but does not recognize any domestic partnerships.

Westfield College Director of Marketing Janet Garcia said the school has a similar taxation policy for same-sex couples as BC.

“We do not offer health insurance coverage because same-sex marriage is allowed in Massachusetts,” Garcia said. “Therefore, if couples choose to get married, they are covered. However, benefits get taxed at a federal level because of the Defense of Marriage Act.”

Boston University spokesman Colin Riley said BU offers equal benefits to all employees’ spouses, including health and dental plans, retirement plans, life and accident insurance, disability and tuition remission.

“Since same-sex couples and opposite-sex couples can both marry in the Commonwealth of Massachusetts, we treat both the same, and that’s been the case since the date of that ruling,” Riley said.

Representatives from gay-rights organizations said the increase in the benefits provided to same-sex couples is encouraging, but said they hope to see even more schools adopt equal benefit programs.

“In Massachusetts, we have legal marriage for same-sex couples, so most universities and companies extend them the same rights,” said MassEquality spokeswoman Melissa Threadgill. “It’s always a step forward when a university or institution decides to accept a loving same-sex couple.”