Gov. Andrew Cuomo and state lawmakers on Monday agreed to amend a bill that will create a commission to investigate misconduct by the state's prosecutors based on concerns over the legislation's constitutionality.

The amendment removes provisions of the bill that were thought to have violated the separation of powers between branches of state government, expanded the role of the judiciary beyond what's in the state constitution, and possibly disrupted the work of the state's prosecutors.

Cuomo signed the bill Monday evening with several agreed-upon changes to address concerns over the bill's constitutionality from the state's judiciary and General Counsel Leslie Dubeck of Attorney General Barbara Underwood's office. The amendment will be approved at the beginning of the legislative session in January.

“At a time when the voices of those alleging misconduct and unchecked power within our criminal justice system have reached a fever pitch and the need to reassure New Yorkers that their confidence in our justice system is not misplaced, a bill intent on doing just that must be embraced,” Cuomo wrote in the approval message for the bill.

The bill, as passed by the legislature in June, required Court of Appeals Chief Judge Janet DiFiore to appoint three active judges to the 11-member commission. Six of the 11 members were to be appointed by the legislature. That commission would investigate complaints of misconduct by prosecutors and refer their findings and a recommendation to the governor.

If a prosecutor disagreed with a decision from the commission, they were allowed in the original legislation to ask the Court of Appeals to review it. The legislation also prohibited the commission from interfering with an active investigation or case.

All of those things were changed Monday as part of the agreement between Cuomo and lawmakers.

DiFiore will no longer be required to appoint active judges because of a constitutional conflict that prohibits those judges from serving on such a commission at the same time. She will instead be allowed to appoint retired judges, who do not hold the same conflict. The Court of Appeals will also no longer review decisions by the commission. That responsibility will instead go to the Appellate Division.

The Legislature will no longer have a majority of appointments to the commission. There were concerns that having a group appointed mostly by the legislature to oversee an executive office, such as a district attorney, would not be constitutional. In the amended version, no one has more members than the executive branch, according to Cuomo's office.

Language will also be included in the amendment that provides more protection for district attorneys from interference in an active investigation or case. Details on that language were unavailable, but according to Cuomo's approval message, the changes would protect victims, witnesses, and the work of prosecutors.

“This potential for abuse would be amplified by the fact that this bill would make public all files provided by a prosecutor to the commission, even while an active investigation is underway; the potential exposure to victims, witness, and a prosecutor's case would be immeasurable,” Cuomo wrote. “This intrusion into active investigations would undermine, rather than support, our criminal justice system.”

The changes are not expected to stop a constitutional challenge from the District Attorneys Association of the State of New York, which is expected to file a motion for declaratory judgement on the constitutionality of the bill in the coming weeks, if not days. A group of district attorneys met last week to begin preparing the litigation.

Albany County District Attorney David Soares, who is president of DAASNY, also asked the state's district attorneys and their assistants to decline serving on the commission until the litigation is resolved. He argued in a letter sent last week that accepting an appointment to a potentially unlawful panel could contradict their role as law enforcement officers.

Soares criticized Cuomo for approving the legislation after Dubeck's memo last week warned of the bill's constitutional flaws, which were not addressed entirely by the amendment.

“Sadly, today the governor, who previously served as the attorney general of the state, after requesting and receiving an opinion from the current attorney general that stated that the legislation is flagrantly unconstitutional, chose to ignore all of these concerns and signed the bill into law,” Soares said. “Everyday, in courtrooms all over the state, prosecutors adhere to their oaths and defend our constitution. As a result of today's events, DAASNY has little choice but to defend the constitution in court yet again—by mounting a vigorous challenge to the enactment of this misguided legislation,”

DAASNY has lobbied against the legislation since it was first introduced in 2015. It instead supported improvements to the state's current system of disciplining attorneys. Each Appellate Division currently has a grievance committee to review complaints against attorneys, including prosecutors.

Sen. John DeFrancisco, R-Syracuse, was one of the bill's sponsors. He said in a statement on Monday that the commission will supplement the work of those committees to better address complaints of prosecutorial misconduct.

“It's clear the current grievance system has not worked, and the liberties of those at stake in criminal prosecutions call for a greater level of protection,” DeFrancisco said.

The bill's other sponsor, meanwhile, is confident the legislation will survive judicial review. Assemblyman Nick Perry, D-Brooklyn, said last week that he was not concerned about the challenge.

Perry said in a statement after the bill's approval Monday that the legislation is not intended as an attack on prosecutors who overwhelmingly serve without misconduct, but instead as a way to root out the bad apples.

“This bill, for sure, is a direct attack on a serious, and surely unintended flaw in our criminal justice system that contributed to New York state's unenviable reputation as a leader in convicting innocent men and women, often times due to the unscrupulous misconduct of a handful of bad prosecutors across our great state who cared more about getting a conviction rather than justice,” Perry said.

The legislation is scheduled to take effect in January after lawmakers approve the amendment. The commission is expected to cost $5.5 million, according to the original legislation.