BOSTON -- A federal judge on Thursday apologized to a transgender inmate who has waited years for a ruling on whether she can get a taxpayer-funded sex-change operation.

Michelle Kosilek, a convicted murderer, first sued the Massachusetts Department of Correction 11 years ago. Two years later, U.S. District Judge Mark Wolf ruled that Kosilek was entitled to treatment for gender-identity disorder, but stopped short of ordering surgery to complete Kosilek's transformation into a woman.

Kosilek sued again in 2005, arguing that the female hormones she was receiving were not enough to relieve her anxiety and depression. Kosilek argued that the surgery was a medical necessity and that the Department of Correction was violating her constitutional rights by refusing to provide the operation.

Since 2006, Wolf has heard hundreds of hours of testimony from medical experts and others, but has not issued his ruling.

On Thursday, as Kosilek's lawyers made additional arguments citing recent rulings in other transgender cases, Wolf apologized for taking so long.

"I deeply regret that my decision in this case has not yet been issued," he said.

Wolf, the chief judge at U.S. District Court in Boston, has handled a number of noteworthy cases recently.

He presided over the trial of former House Speaker Salvatore DiMasi, who was convicted in June of conspiracy, extortion and other charges. He also is scheduled to rule on a request for a new trial in the federal death penalty case of Gary Sampson, a drifter from Abington who was sentenced to death after killing three people during a weeklong crime rampage in 2001.

Wolf told attorneys for Kosilek and the Department of Correction that he knows the case "is extremely important ... to all parties."

"I will continue to keep that in mind," he said.

Kosilek, born as Robert, was convicted of killing his wife in 1990. Kosilek, now 62, legally changed his name to Michelle in 1993. She has received hormone treatments and lives as a woman in the state prison in Norfolk, a medium-security, all-male facility.

During Thursday's hearing, Kosilek's lawyer, Frances Cohen, said a recent ruling by the 1st U.S. Circuit Court of Appeals in the case of another transgender inmate bolsters Kosilek's claim that prison officials are violating her constitutional rights by denying her the surgery.

In the ruling, the appeals court upheld a lower court judge who found the state Department of Correction had shown deliberate indifference to inmate Sandy Battista's medical needs by repeatedly denying her request for female hormone treatments. The court found that the department's claim that its decision was based on security concerns had been "undercut by a collection of pretexts, delays and misrepresentations."

Prison officials have cited similar security concerns in the Kosilek case, saying that allowing her to have the surgery could make her a target for sexual assaults by other inmates.

Cohen said the security concerns were also a pretext in the Kosilek case.

"It is remarkably similar to what we've been hearing in this court for quite some time," she said.

But Richard McFarland, a lawyer for the Department of Correction, said the prison officials are genuinely concerned about security problems if Kosilek is allowed to have the surgery.

He cited the testimony of former DOC Commissioner Kathleen Dennehy, who said the department's decision to deny the surgery had nothing to do the costs – about $20,000 – or the political ramifications of allowing an inmate to have a taxpayer-funded sex-change operation.

McFarland said the DOC has given Kosilek hormone treatments, female items and psychotherapy to help her deal with gender-identity disorder.

"We argue that the treatment provided to Miss Kosilek is adequate" and the surgery is not a medical necessity, McFarland said.

Wolf asked both sides to submit additional arguments in writing by Sept. 16. He tentatively scheduled another hearing for Oct. 11.