"The President, in remarks delivered yesterday in New York, condoned police misconduct regarding the treatment of individuals placed under arrest by law enforcement," DEA Acting Administrator Chuck Rosenberg wrote in a message to DEA's "Global Distribution" list Saturday.
"In writing to you, I seek to advance no political, partisan, or personal agenda. Nor do I believe that a Special Agent or Task Force Officer of the DEA would mistreat a defendant. I know that you would not," Rosenberg added. "So, why do I write? I write to offer a strong reaffirmation of the operating principles to which we, as law enforcement professionals, adhere. I write because we have an obligation to speak out when something is wrong. That's what law enforcement officers do. That's what you do. We fix stuff. At least, we try."
Trump, in a speech meant to focus on effort to combat the brutal gang MS-13 Friday, told police officers to be "rough" with suspects.
"When you see these thugs being thrown into the back of a paddy wagon. You just see them thrown in -- rough. I said, 'Please don't be too nice,'" Trump said to applause, referring to officers shielding prisoners' heads with their hands. "Like, don't hit their head and they've just killed somebody, don't hit their head. I said, 'You can take the hand away, OK?'"
White House press secretary Sarah Huckabee Sanders dismissed the Rosenberg email on Tuesday.
"It wasn't a directive, it was a joke," Sanders said during the White House press briefing. "There is a very big difference."
She added: "I think you guys are jumping and trying to make something out of nothing. He was simply making a comment, making a joke and it was nothing more than that."
Melvin Patterson, spokesman for the DEA, told CNN on Tuesday that the email was "just to reinforce our DEA core values and reinforce what everyone at DEA needed to hear, in light of the president's comments that were broadcast."
Rosenberg's email was first reported by the Wall Street Journal.
Rosenberg, a holdover from the Obama administration, became acting head of the department tasked with combating drug smuggling in the United States and abroad in 2015 when former DEA chief Michele Leonhart resigned. The Trump administration has not nominated anyone for that job and the Trump transition team told reporters in January that Rosenberg would be one of the Obama administration officials to staying to work under Trump.
The comments -- received with applause at the time -- were quickly rebuked by police departments across the country, including the Suffolk County Police Department in New York, whose officers provided the backdrop to Trump's remarks.
The Suffolk County Police Department said in a statement, "As a department, we do not and will not tolerate 'rough(ing)' up prisoners."
"The Suffolk County Police Department has strict rules and procedures relating to the handling of prisoners, and violations of those rules and procedures are treated extremely seriously," the department said.
Departments from New York to Boston to Los Angeles all condemned the remarks and said they did not reflect their teachings or guidelines.
"I was very concerned when I first heard those remarks because I believe it reinforces a very negative stereotype of police that we've been trying to overcome. That is, that police use excessive force on a regular basis, we violate people's constitutional rights," Philadelphia's former police commissioner Charles Ramsey told CNN on Monday.
Initially, the White House had no response to the growing controversy, but White House press secretary Sarah Huckabee Sanders told reporters on Tuesday that Trump was "joking" when he made the comment.
"I believe he was making a joke at the time," she said.
Blaming the comment on Trump's sense of humor tracks with the White House and Trump campaign's history of deflecting a controversial comment by arguing that president was joking.
Months after Trump urged Russia to hack into Hillary Clinton's email account to find the 33,000 emails she deleted before turning over her messages to the Justice Department, former White House press secretary Sean Spicer told reporters the then candidate "was joking at the time."
"We all know that," Spicer said.
In the email, Rosenberg goes on to list the core values of the DEA, which include "Rule of Law," "Respect and Compassion" and "Integrity."
"This is how we conduct ourselves," he writes. "This is how we treat those whom we encounter in our work: victims, witnesses, subjects, and defendants. This is who we are."
Some officers defended Trump in the face of criticism.
Detective Stephen Loomis, president of the Cleveland Police Patrolmen's Association, a union representing Cleveland's rank-and-file police officers, told CNN there is "unwavering" support for Trump from law enforcement agencies across the country.
"Not surprisingly, (Trump's) comments have been completely taken out of context by the racially exclusive and divisive profiteers seeking to call into question his support of all law abiding citizens and the law enforcement that live and work among them," he said.