A whistle-blowing cop says arrest quotas in one Bronx precinct have the Finest there so angry that the locker room has to be guarded “around the clock” to prevent vandalism.

In a civil-rights suit filed this morning, veteran cop Craig Matthews says the quota system at the 42nd Precinct “has pitted police officers against each other, straining professional relationships and diverting resources away from law enforcement activities.”

He says cops who “comply” with the program “have had their precinct lockers dislodged and overturned, with the lockers sometimes being placed in the shower or their locks being plastered shut.”

“This practice of ‘locker flipping’ has escalated to the point where on-duty police officers are now assigned to guard the precinct’s locker room around the clock,” court papers say.

Matthews, a 14-year veteran, made the stunning revelation in a Manhattan federal court filing that charges he’s “been subjected to a campaign of retaliation and harassment” for telling top brass at the precinct about the “highly developed quota system” employed by “mid-level supervisors” there.

The suit — which targets the city, Police Commissioner Ray Kelly, precinct commander Deputy Inspector Jon Bloch and Lt. Mark Sedran — seeks a court order that they “cease all actions in retaliation for (Matthews’) protected speech,” plus unspecified damages.

Matthews says supervisors use color-coded computer reports to track each officer’s amount of arrests, summonses and highly controversial “stop-and-frisks” — which one supervisor allegedly described as “worth their weight in gold.”

“Current reports use black ink to identify officers who are meeting quotas, silver ink to identify officers who are meeting only some quotas and red ink to identify officers who are not meeting quotas,” according to court papers.

Matthews says cops “are constantly pressured to meet the quotas, and those who do not are subject to punishment including undesirable assignments, the loss of overtime, denial of leave, separation from partners and poor evaluations.”

The suit says Matthews notified his commanding officers about the quota program — which began in 2008 — “on at least four occasions.”

After his first three complaints, in 2009, then-precinct commander Captain Timothy Bugge allegedly told Matthews that he had spoken to Sedran, who is Matthews’ platoon commander, “and that the situation was handled.”

“In fact, the quota system continued, with Lt. Sedran saying in a roll call that he would use it secretly,” court papers charge.

Matthews says Sedran also began “constant and personal” harassment that was so severe Matthews began “to suffer both mentally and physically,” including a heart-attack scare that sent him to the emergency room, where his symptoms were blamed on “extreme stress.”

In January of last year, Matthew says he told Bloch — who took over the precinct in 2010 — about he quota system and how “it was causing unjustified stops, arrests and summonses,” and “having an adverse effect on the precinct’s relationship with the community.”

In response, Bloch allegedly “became irate and ordered Officer Matthews and the others (at the meeting) out of his office.”

Since then, Matthews says he’s been subject to “heightened retaliation” that includes risky assignments such as being forced to process 13 prisoners without any back-up.

Matthews also says that during a Jan. 8 roll call, Sedran “threatened” him, saying: “If you come after me, I will come back after you harder.”

According to his suit, Matthews has gotten more than 20 awards since being assigned to the 42nd Precinct in 1999, and until recently “consistently received positive annual reviews” that praised him as “incorruptible,” “always desirous and willing to work” and “a valuable asset.”

In 2010, however, he got an overall rating of 3 out of 5, “which is the lowest passing score and is significantly below his normal rating.”

The review was also “highly critical of his outspokenness,” alleging that he’s “difficult to work with, questions his assignments and wants to debate every issue.”

And earlier today, Matthews was slapped with an evaluation that gave him an “extraordinarily low” rating of 2.5 “that subjects him to close monitoring and puts him at risk of being fired.”

Matthews is being represented by the New York Civil Liberties Union, which said it also plans a second suit “seeking to have the quota system declared illegal under New York labor law.”

The NYCLU cited recent scandals in which a cop used secret audio recordings to expose arrest quotas at the 81st Precinct in Brooklyn, and testimony by a former Queens narcotics detective who said he and other cops planted cocaine on innocent people to boost their arrest numbers to meet quotas.

“Quotas lead to illegal arrests, summonses, and stop-and-frisks, and they undermine trust between the police and residents,” NYCLU lawyer Christopher Dunn said.

“Officer Matthews chose to expose this abusive system, and in response his supervisors have made his life miserable. We believe quotas are a problem throughout the NYPD, and we’re confident the courts will put a stop to this unlawful retaliation.”

The city Law Department didn’t immediately respond to a request for comment.