Thursday, January 22, 2009 – updated: 10:08 am PST January 23, 2009 (KTVU)

OAKLAND, Calif. -- The Oakland Police Department is facing increased scrutiny amid new allegations of misconduct as a police captain currently serving as head of internal affairs was placed on administrative leave over charges he kicked a suspect so hard that the man later died.

What has already been a chaotic start to 2009 because of the recent riots surrounding protests against the BART police shooting of Oscar Grant took a significant turn for the worse for the Oakland Police Department.

KTVU news, in partnership with the Chauncey Bailey Project, has learned that the FBI has launched a wide-ranging investigation of the department.

Department officials confirmed Thursday that the FBI is investigating an unspecified case from the year 2000 involving an unnamed commander who is now on administrative leave.

Sources tell KTVU the commander is Captain Ed Poulson, head of internal affairs. He's alleged to have kicked a drug suspect so badly near the corner of 73rd and Holly Street that the suspect later died of his injuries.

A coroner's report shows the cause of death for 36-year old Jerry Amaro was bronchopneumonia and hemothorax caused by multiple rib fractures due to blunt trauma to the chest.

The report obtained by the Chauncey Bailey Project quotes several informants, including the doctor who treated Amaro, as saying that he told them he was injured in a police beating.

An internal affairs investigation at the time found that Poulson ordered other officers to lie about his involvement. Poulson was later suspended for two weeks.

But after Poulson was promoted to captain and given the internal affairs command, sources tell KTVU that other officers were outraged that someone who had been punished for interfering in an internal affairs investigation was later promoted to head that division.

Those officers informed the FBI, which initiated the current federal investigation.

Oakland City Councilman Larry Reid, the chair of the Public Safety Committee, told KTVU he is floored by word of an FBI investigation.

"The city is getting a black eye. I mean, it's all over the United States, said Reid. Like I said, [if you’re in] Washington DC and you tell them you're from Oakland…they feel sorry for you. It just goes on and on and on. And it's very frustrating."

Reid said he takes this latest allegation and the FBI investigation seriously.

"That's one of the things that I was talking to Asst. Chief Jordan about tonight," said Reid. "And certainly we'll be calling the city attorney's office to get this issue into closed session, so we as a council can understand these issues. And let the chief and the FBI do their job."

Along with the Poulson investigation, sources say the FBI is also looking into the Chauncey Bailey murder case and whether it was investigated properly. Other incidents getting attention are the case of former city administrator Debra Edgerly -- who allegedly warned a nephew who was a gang member of an impending drug raid -- and the recent scandal involving search warrants allegedly falsified by 11 officers.

There is also a whistleblower complaint against Police Chief Wayne Tucker, who is alleged to have promoted former union president Bob Valladon to acting sergeant so Valladon could retire at a higher pay grade and Tucker could avoid a no-confidence vote by officers.

And lastly there allegations of sexual harassment filed against Deputy Chief Jeff Loman by a subordinate female officer.

Reid made it clear that he wants all of these issues to be addressed.

"Hopefully, the image of the police department and the image of our city will be one that we can articulate," said Reid. "That this is an incredible city that we live in in the state of California. And that we're not trying to hide anything, We're bringing the issues forward."

Oakland Police Chief Tucker has issued a statement saying "The men and women who put on the uniform are held to high standards of ethical conduct and performance. Please do not allow recent allegations of misconduct to overshadow the successful policing efforts achieved by Oakland Police Department personnel on a daily basis."

Sources tell KTVU Captain Poulson turned in his gun and badge Thursday and is on paid administrative leave.

Oakland Defense Attorney John Burris told KTVU Thursday night he was once involved in the alleged beating case of Jerry Amaro, but that the case never got anywhere.

He told KTVU there was a massive cover-up. Burris called OPD "a cesspool."