The resignation Tuesday of the dean of the Berkeley Divinity School, an Episcopal seminary that is affiliated with the Yale Divinity School, comes after a Yale-initiated audit showed misappropriation of Berkeley funds by the dean.

Berkeley Dean William R. Franklin, who also serves as an associate dean at the Yale Divinity School, announced that he will leave Yale at the end of this year.

Following the audit, the University will now no longer allow Berkeley to build a chapel on the campus of the Yale Divinity School. Originally Yale had given permission for Berkeley to build a new chapel on the main Yale campus.

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

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

“Franklin raised three million dollars 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. 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 Yale administrative source said.

This summer, Yale officials called for an audit of the Berkeley funds, and the audit then revealed practices that were not in line with University policies.

On Tuesday, the Hartford Courant outlined the alleged misappropriation by Franklin, citing the confidential audit.

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 Harvard Medical School 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 friends, the Courant reported Wednesday.

Greer said the problems stem from general financial procedures at Berkeley that stretch beyond Franklin.

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 Franklin’s resignation was a personnel matter and that the Yale administration cannot discuss it.

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 the dean and rebutting the charges, Greer said.

“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,” Christian R. Sonne, chairman of the board of trustees of the Berkeley Divinity School, said in a statement. “[Franklin] has been an extraordinary leader of Berkeley Divinity School, and we are deeply grateful for what he has accomplished.

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

“The Berkeley Board of Trustees does not meet in secret. The [Yale] Divinity School Dean [Rebecca Chopp] 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 ten years and not examine it carefully … He did not devise the financial system at the Berkeley School or the perks he gained.”

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

Three weeks ago, in answer to speculation that Yale and Berkeley might merge or part ways, Chopp told the News 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. One possible solution, Greer added, is that the two schools will jointly appoint the Berkeley School Dean, but either school will be able to remove the Dean unilaterally.

Franklin, who has been dean of Berkeley for four years, will assume a new position with the Episcopal Diocese of New York.

–Staff Reporter Elise Jordan contributed to this report.