The New York health department "misled the public", said state comptroller Thomas DiNapoli in his 58-page report.
Mr Cuomo last year admitted to a "delay" in reporting but did not apologise.
The politician, a Democrat, resigned in August after an inquiry found he sexually harassed multiple women.
Mr Cuomo has repeatedly denied the sexual harassment allegations against him. In January, prosecutors in New York dropped a groping charge against the former governor, saying the accuser was "credible" but there was not enough evidence to bring the case to court.
In the early days of the pandemic, Mr Cuomo was lauded for his handling of the pandemic after New York experienced one of the worst initial covid outbreaks in the country. In October 2020, he published American Crisis, a book of "leadership lessons" from that time.
It was later revealed that during his administration, the state health department had significantly undercounted nursing home deaths. This new report, released on Tuesday, marks the third state inquiry into how Mr Cuomo's administration failed to be transparent about the true tally.
"The public was misled by those at the highest level of state government through distortion and suppression of the facts when New Yorkers deserved the truth," Mr DiNapoli said in a statement.
He called the findings "troubling" but his audit did not say whether the undercount was due to poor-quality data or a "deliberate decision".
The audit found Cuomo's health department failed to meet its "ethical" and "moral" imperatives to act transparently in counting deaths between April 2020 and February 2021.
"Rather than providing accurate and reliable information during a public health emergency, the department instead conformed to the executive's narrative, often presenting data in a manner that misled the public," the report said.
According to the audit, almost 14,000 people died in nursing homes due to covid between March 2020 and May 2021.
An earlier report found that the undercount was due, in part, to a controversial policy that included only those who died in residential facilities in the state's nursing home death toll - excluding residents who died outside those facilities, including in hospitals.
In a 12-page statement to the New York Times, the health department rejected the report, saying criticism of Mr Cuomo's administration should not be conflated with the work of health department staff.