An Episcopal seminary associated with the Yale Divinity School has seen its dean resign amid allegations that he misappropriated tens of thousands of dollars, using funds for such purposes as his daughter’s Harvard Medical School tuition.

The controversy at the Berkeley Divinity School, an Episcopal seminary, comes as the current affiliation agreement between Berkeley and Yale is up for renewal, raising questions about the future of the two schools’ relationship.

Dean R. William Franklin resigned his position at Berkeley in mid-December after the Hartford Courant reported that a Yale-initiated audit showed misappropriation of funds. Franklin has left Yale and is now employed by the Episcopal Diocese in New York City.

Amid the controversy, Yale also has rescinded permission for Berkeley to build a chapel on the main campus of the Yale Divinity School, which may require Berkeley to return $3 million dollars in pledges and gifts to donors.

“We decided that given the circumstances, we decided that maybe this was not a good idea,” a Yale administrative source said of the plans for the chapel.

Berkeley administrative assistant Jeanne Moule, who worked for Franklin since he arrived at Yale in 1998, said that working for Franklin was a wonderful experience.

“It is shocking what happened,” Moule said. “Having known him and worked so closely with Dean Franklin for the past four years, I certainly couldn’t believe he had been accused in that way. He is so admired and respected here by everyone.”

The Hartford Courant outlined the alleged misappropriation by Franklin, citing the confidential audit from last summer. The Courant said the audit showed that Franklin had mismanaged tens of thousands of dollars, using some of the funds to pay for his daughter’s education and personal expenses including a trip to Colorado and dry cleaning.

Connecticut Attorney General Richard Blumenthal has launched an investigation into Berkeley’s use of charitable funds.

Blumenthal said he was informed of the Yale audit and was contacted by people with knowledge of the situation. The information he received, he said, led him to believe that further investigation was necessary.

“The investigation will focus on whether money may have been improperly used or misappropriated,” Blumenthal said. “We will be reviewing documents relating to how money was used and how it was obtained.”

Rowan Greer, a professor emeritus at the Divinity School, said the problems stem from general financial procedures at Berkeley that stretch beyond Franklin.

“The big problem was that neither Berkeley’s financial procedures [nor] perks for the dean actually conformed to Yale,” Greer said. “What is happening now is that Berkeley is trying to conform specifically with Yale.”

Greer said that in September there was a meeting at which Levin upbraided the school and the dean for their financial practices.

“Basically, there was an attempt on part of the central administration to remove the dean of Berkeley,” Greer said.

Levin said Yale participates in the selection of the Berkeley dean but has no disciplinary power over the office. Levin said the Yale administration cannot discuss Franklin’s resignation.

Greer said the Berkeley Board of Trustees established a finance committee to try to conform to University standards and to conduct an independent audit. In October the Berkeley board of trustees passed a motion exonerating Franklin and rebutting the charges of financial mismanagement, Greer said.

Greer said Christian R. Sonne, chairman of the Board of Trustees of the Berkeley Divinity School, asked him to refrain from further contact with the media and said the Berkeley board does not want Greer to be a spokesman for Berkeley anymore.

“Upon investigation, many of the matters referred to in the auditors’ report have proven to be incorrect or misleading, while many others have proven to be perfectly appropriate, and there has been no misappropriation of funds,” Sonne said in a statement. “[Franklin] has been an extraordinary leader of Berkeley Divinity School, and we are deeply grateful for what he has accomplished.”

Officers of the Berkeley Divinity School Board did not return repeated phone calls for comment. John Berke of the public relations firm Robinson, Lehrer, Montgomery in New York City, is the spokesman for Berkeley.

“The Hartford Courant wrote a story that is erroneous which suggests that there was some problem when that is simply not the case,” Berke said. “Yale University conducted an internal confidential audit of an affiliated school for the first time in 10 years as part of the process established when Berkeley became affiliated with Yale 20 years ago. That audit — as with all audits — identified some accounting issues.”

Greer said he believes that the financial system of Berkeley, while messy, is not illegal or particularly out of the ordinary, saying the system has been in place for ten years.

“The Berkeley Board of Trustees does not meet in secret. The [Yale] Divinity School dean and two other appointed Yale officials attend all the meetings,” Greer said. “Franklin’s basic mistake was to trust a system that has been in place for 10 years and not examine it carefully — He did not devise the financial system at the Berkeley School or the perks he gained.”

Franklin’s departure is not the only change in Berkeley’s long-term plans.

Greer said that on Dec. 14, Yale President Richard Levin withdrew an offer for the Berkeley school to move into new Yale Divinity School buildings.

“Franklin raised $3 million for those buildings, and that will now all have to be returned,” Greer said.

The Yale administrative source said Berkeley still can put its administrative offices on the Yale campus, just not a new chapel. The source said none of the funds have come directly to Yale and added that Berkeley controls and has access to any funds that have been raised.

“I think they are mostly pledges,” the source said.

In a later interview, Greer confirmed that the $3 million was not necessarily hard cash.

“A lot of it [the money] is in pledges,” Greer said. “All I know is that Berkeley retained control of the money that had been raised.”

There also has been discussion this year about the contractual agreement between the two schools.

In November, in answer to speculation that Yale and Berkeley might merge or sever ties, Divinity School Dean Rebecca Chopp said that a task force was examining the relationship between the two divinity schools because their affiliation agreement is up for renewal this year.

Berkeley retains an independent board of trustees and administration, but its students are fully enrolled in the Yale Divinity School.

Greer said there will be another meeting on Jan. 24 between Berkeley and Yale officials.

“We are hoping we can work out the remaining details of a revised affiliation agreement,” Levin said.