Proceed with care. That’s what bankers, accountants and wealth managers are telling same-sex couples considering financial changes because of the Supreme Court’s rejection of a federal law denying them benefits.

After years of fighting for equal tax-and-benefit treatment, married couples now await guidance on how the Internal Revenue Service and federal agencies will implement the ruling. Without it, those who file for tax refunds may end up paying more, not less.

Married couples in states that don’t recognize gay marriage and those who delayed filing their 2012 returns in anticipation of the court’s decision in June are pressing for clarity. Spouses computing whether to seek refunds from prior returns see the three-year statute of limitations for amendments closing as they look to the IRS for details.

“We are desperately awaiting that guidance,” said Shari Levitan, chairwoman of the New England private wealth services group at Holland & Knight LLP in Boston. “The major question for clients is for returns that are still open, and even those that are beyond the statute of limitations, can they be amended?”

Without IRS guidance, couples who extended their 2012 return deadline to Oct. 15 and who live in a state that doesn’t recognize their marriage will probably file their federal returns jointly and disclose they are doing so based on the court’s decision, Levitan said. She serves high-net-worth clients, about 10 percent of them same-sex couples.

Taking ‘Risk’

“That’s a risk,” because the IRS could deem they filed incorrectly, she said.

The IRS said June 27 that it was reviewing the court’s decision and would “move swiftly to provide revised guidance in the near future.” The agency referred to this statement when asked yesterday to comment on the timing of any guidance.

Amending returns may subject some same-sex couples to higher taxes because of the so-called marriage penalty, which generally affects taxpayers when one or both are in the top income-tax bracket, or if both make relatively similar salaries. It also could open tax returns to scrutiny.

“You have to make sure there’s nothing else in your return that would cause the IRS to look at it,” said Nanette Lee Miller, co-head of New York-based accounting firm Marcum LLP’s practice for gay, lesbian, bisexual and transgender couples.