New York (CNN) -- New York state's top police official announced Wednesday he was quitting, the second acting superintendent to step down in as many weeks.
In a letter to embattled Gov. David Paterson, Pedro Perez denied his resignation was connected to the ethics scandals embroiling Albany.
"My retirement is not premised on the current investigation by the Attorney General [Andrew Cuomo], as I know my decisions were honest and rightly motivated," Perez said in the letter, which the New York State Police released.
Perez's resignation takes effect Friday and ends his 28-year career as a police officer, his letter said.
His predecessor, Harry Corbitt, quit March 2, less than a week after the abrupt resignation of Denise O'Donnell as New York's deputy secretary for public safety. O'Donnell said Corbitt had misled her about state police involvement in a scandal involving a top aide to the governor.
The Democratic governor has been mired in controversy since news reports emerged alleging an aide was involved in a domestic violence incident with a woman and that state police later allegedly pressured the woman to keep quiet.
The aide, David Johnson, has been suspended without pay.
Corbitt has said he did not dispute O'Donnell's account of what he told her but said, "The conclusions she appeared to draw from these statements were incorrect."
Separately, the New York State Commission on Public Integrity on March 3 accused Paterson of an ethics violation for allegedly accepting free tickets to the first game of last year's World Series.
The commission also said Paterson lied under oath about intending to pay for the tickets.
Paterson's spokesman, Peter Kauffmann, resigned the next day, saying he could not keep doing his job "in good conscience."
The governor's office said it was reviewing the commission's findings.
"Gov. Paterson maintains his innocence and intends to challenge the findings of the commission both with respect to the law and the facts," the office said.
The governor could face up to an $80,000 fine for violating the state's gift ban for public officials, and up to $10,000 if he is found to have used his official position to secure unwarranted privileges.
The commission has asked Cuomo, the state's attorney general, and the Albany County district attorney to investigate.
Cuomo is a possible Democratic contender for the governor's office in 2010.
Paterson, a former New York lieutenant governor who stepped into the governor's mansion when Eliot Spitzer resigned in 2008 over a prostitution scandal, has abandoned his campaign for election to a full term, saying it was not the "latest distraction but an accumulation" of obstacles behind his decision.
CNN's Mark J. Norman contributed to this report.