Before becoming mayor, he opposed a proposal to create a civilian board to review police conduct and famously rallied a rowdy demonstration of officers against the idea.
GPD rejects these remarks and continues to serve with respect.
But the Suffolk County Police Department did not seem to subscribe to Trump's advice.
Mr. Trump has repeatedly declared his intolerance for criticism of police and immigration officials by rights groups.
At the same time, the department is dealing with a historic surge in violence.
The president's comments are disgraceful and anathema to responsible policing and the Rule of Law.
The White House did not return messages seeking comment on Saturday.
The Suffolk County Police Department said they do not tolerate the "roughing up of prisoners" in response to President Trump's address to police on Long Island on Wednesday, in which the president said cops should treat subjects violently.
"The NYPD's training and policies relating to the use of force only allow for measures that are reasonable and necessary under any circumstances, including the arrest and transportation of prisoners", commissioner James O'Neill said in a statement.
"Violations of those rules are treated extremely seriously", the department wrote.
The US President was speaking to a room full of police in NY on Friday when he spoke dismissively of arresting officers who use their hands to protect suspects' heads when putting them in police cars. You do something wrong, you're in more jeopardy than they are. "This disgusting call for violence is exactly why so many communities of color don't trust police!" Gray left the vehicle with severe neck injuries, and his subsequent death triggered rioting.
"The ability of law enforcement officers to enforce the law, protect the public and guard their own safety, the safety of innocent bystanders, and even those suspected or apprehended for criminal activity is very challenging", the statement reads. In his words "It's an unfitting comment for a president of the United States, but it's a fitting comment for this president who is unfit to be president". The president has often spoken about the "criminal cartel" MS-13 - which has origins in Central America - and its relationship to illegal immigration.