His opponents, meanwhile, accuse Chief Juan Carlos Bonilla of firing his rivals, including those who signed a 2004 evaluation saying Bonilla was suffering from severe anxiety and needed hospital care and psychotherapy.
That same year, Bonilla, nicknamed "the Tiger," was acquitted on a murder charge after the department's internal affairs office accused him of running a death squad when he was a top regional police official.
"I have information that there are some who are meeting in some place and planning to take action," Bonilla told Radio HRN late Wednesday. "We are ready for them. We will meet them head on."
One top police official told The Associated Press there is "enormous discontent" in the department, and said at least 30 officers have been meeting for several weeks to take measures to get rid of Bonilla, who was appointed in May after his predecessor served only six months.
The police chief position has become a revolving door over recurring allegations of officers involved in drug trafficking, murder and kidnapping in this Central American country of 8 million people.
The official said the opponents of Bonilla plan to first work through the judicial system, asking President Porfirio Lobo to dismiss the chief for "irregularities and crimes." If that doesn't work, they are considering a takeover of police headquarters, the official said.
"It depends on what the president does to keep this from happening in the coming days," said the official, who agreed to discuss the situation only if his name was not used, saying he feared reprisal.
Neither Lobo nor Security Minister Pompeyo Bonilla, who is no relation to the police chief, responded to requests for comment from the AP.
The dispute has been fueled by leaked documents implicating both sides. Earlier this week, Honduras media printed a list of 99 officers who are being suspended with pay as part of a cleanup, including Bonilla's predecessor, Ricardo Ramirez del Cid, two other former police chiefs, two generals and three high-ranking commissioners.
The official who spoke anonymously and is not one of the officers on the list said Bonilla is sidelining people who have more experience and seniority.
The AP obtained internal police documents showing that Bonilla in 2004 ranked last on a list of 12 officers seeking promotion, noting that his qualifications were "insufficient" and recommending that he receive psychotherapy and medical help.
Three of the officials who signed the report are on Bonilla's suspension list, including Ramirez.
Security Ministry spokesman Hector Ivan Mejia confirmed Thursday that the documents are authentic but questioned the timing of their release.
"If they knew this eight years ago, and two of the people who signed it were police chiefs, why didn't they do anything?" Mejia said. "You can't claim something eight years later if you didn't doing anything about it at the time."
He said Bonilla would not be doing any interviews.
After Bonilla was named police chief May 21, a decade-old report resurfaced that named him in at least three killings or forced disappearances between 1998 and 2002 and listed him among several officers suspected in 11 other cases. Only one of those allegations against Bonilla led to murder charges, however, and he was acquitted in 2004. The verdict was upheld by Honduras' Supreme Court in 2009.
The U.S. State Department in August decided to withhold funds to law enforcement units directly supervised by Bonilla while it investigated the death-squad allegations.
Commissioner General Santos Simeon Flores said he was indignant to hear in the media that he was let go since he already retired in June.
His name is not on the official list obtained by the AP.
Simeon said the confusion shows the incompetence of the police administration.
"This is what happens when politicians reach into the police ranks and appoint a director and bypass the hierarchy of career, seniority, experience and ability," he said, referring to Lobo's appointment of Bonilla. "This isn't a cleanup, it's a whim."