UPDATED 06/19/12 – 5:05 p.m.

CHICAGO (CBS) — After months of investigations into an overcrowding scandal at the Cook County morgue, the office is undergoing a major shakeup.

As CBS 2’s Mai Martinez reports, Chief Medical Examiner Dr. Nancy Jones will be stepping down at the end of next month, and a top deputy is also on the way out.

LISTEN: WBBM Newsradio’s Regine Schlesinger reports

Jones came under fire back in January for mismanagement, after bodies were found piled up and stacked upon each other at the morgue, at 2121 W. Harrison St.

Also out at the Medical Examiner’s office is Kimberly Jackson, the executive officer at the morgue, who was responsible for indigent burials. Jackson was asked to resign.

Preckwinkle said Kimberly Jackson would be replaced by Daryl Jackson — no relation — a former state health official, effective July 13.

Preckwinkle also announced new health and safety procedures for the Medical Examiner’s office.

“I believe you will see an improvement in the operations of the facility,” Preckwinkle said. “As I’ve said, we’ve done a thorough review over the last six months to try to figure out exactly where we are.”

Preckwinkle also announced that four Medical Examiner’s office employees have been fired.

She says a nationwide search for Jones’ replacement is now underway.

Crowding at the morgue was brought to light after a family’s two-week search for a missing man, whose body was there all along.

Sheila Hostetler, the man’s sister, said even the morgue workers admitted they had the man’s body.

“They were like, ‘OK come get the body,’ and it’s really so heartbreaking,” she said.

Then pictures showing conditions at the morgue came out. Most infamously, a cell phone photo revealed bodies stacked up in blue bags outside an overflowing cooler. Meanwhile, the cooler itself was supposed to hold 300 bodies, but had been filled with 363.

CBS 2 obtained this photo of bagged bodies stacked at the Cook County Medical Examiner’s Office, which is over its storage capacity.

Hostetler said earlier this year that the conditions at the morgue were “even more heartbreaking to us, because he was loved by us, and he did everything that we could to search for him, and to have him there with those as if he’s not loved — like he’s a piece of trash.”

County officials said their employees weren’t completely to blame for the overcrowding.

“The reason we had that many bodies is because the state stopped paying the funeral directors,” said Cook County Chief Administrative Officer Robin Kelly. “175 of those bodies at the time you’re talking about were that type of case.”

Troy Taylor, from House of Branch Funeral Home, said he witnessed the body backlog firsthand.

“Basically bodies being left on top of each other,” he said. “And the smell is just basically outrageous. … I wouldn’t wish that on nobody.”

Taylor said he believes the medical examiner’s office was poorly run and the problems were the result of negligence.

Preckwinkle wouldn’t go that far, but did say “we needed stronger management.”

The overcrowding scandal led to a two-week internal investigation and made the headlines for weeks, and got Jones in a lot of trouble.

In January, Preckwinkle said the findings had left her “disturbed, disappointed, discouraged – but this is a situation that we’re going to get under control, I think, pretty quickly.”

Preckwinkle called for an overhaul of operations.

“We’re taking responsibility for cleaning up operations there, and moving forward,” she said.

At a Cook County Board meeting in March, commissioners were upset when Jones didn’t show up for a discussion of problems at the morgue, though no one specifically mentioned Dr. Jones would lose her job.

“There’s an inescapable perception that she’s hiding,” Commissioner John Fritchey (D-12th) said at the meeting.

Dr. Jones blamed state cuts for the overload and backlog. Since then, state funding to bury the poor has been restored.

In March, the County Board came out with new morgue rules. Bodies have to be buried in 60 days, the Medical Examiner has to present quarterly reports on conditions at the morgue, and the Chief Medical Examiner gets a five-year term rather than an effective lifetime appointment.

This also means whoever is appointed next won’t be able to stay past five years without the board approving another term.

Preckwinkle insisted the office will not be shorthanded after Jones’ and Kimberly Jackson’s resignations, and the other firings.

“The medical examiner’s office has hired eight new employees, and has created a full personnel plan,” she said.

Taylor said he hopes that will make a difference.

“We pray and hope there’s a change coming because it’s past due,” he said.

Preckwinkle said there will also be policy changes. Burial shelves are also being built at the facility to better store the bodies.