By Stephanie Stahl

PHILADELPHIA (CBS) — There were more apologies from Philadelphia officials Monday following revelations the city’s health department mishandled a major COVID-19 vaccination partnership. The deputy health commissioner has resigned and Philadelphia City Council is taking action.

The city’s relationship with Philly Fighting COVID — the group of college students that mishandled vaccinations — is now being investigated.

READ MORE: Man Dead, Another Injured In Shooting At Coatesville Moose Lodge, Police Say

Many have called for Health Commissioner Dr. Thomas Farley to resign, but Mayor Jim Kenney is standing behind him.

“We’re not perfect and we made mistakes,” Kenney said. “We all deeply regret but we are committed to doing better and restoring the public’s faith in the city’s ability to get our residents vaccinated.”

Kenney apologized for mistakes from the health department that’s now being investigated by the inspector general.

It centers on a now-terminated partnership with Philly Fighting COVID, the group that set up a vaccination site at the Pennsylvania Convention Center.

Dr. Caroline Johnson, the acting deputy health commissioner, has resigned following revelations that she gave PFC and the Black Doctors Consortium — another vaccine provider — information that was not available to other applicants.

“She recognized that the emails could be perceived as an unfair advantage to these two potential applicants,” Dr. Farley said. “It appears this was an attempt to move vaccine into people’s arms more quickly and more efficiently.”

The health commissioner says the city will replace the set up at the convention center starting Wednesday and provide the necessary second doses, as it continues to expand its vaccine distribution.

“There’s some level of embarrassment as it relates to the perception of how we do things here,” City Council President Darrell Clarke said.

City Council is calling for vaccination contract reforms in the wake of the controversy and will hold hearings.

READ MORE: Man Found Dead Inside Vehicle After It Crashed, Caught On Fire In Northeast Philadelphia, Police Say

“We need to get answers to make people feel safe,” Councilwoman Cindy Bass said.

Dr. Farley says he takes responsibility and will work with investigators and would resign if asked by the mayor.

“I’ll be happy to leave,” the health commissioner said.

“And I’m not asking you,” Kenney responded. “I think Dr. Farley and the team has done a good job under difficult circumstances.”

The mayor and health commissioner said losing Dr. Johnson was a big loss. She was highly respected and the cornerstone of the vaccination rollout.

But, Dr. Farley says he’s confident his department will be able to move past this controversy and proceed on schedule with vaccinations.

MORE ON CBSPHILLY.COM 

Philadelphia Under Snow Emergency As Nor’easter Expected To Dump Most Snowfall In City In 5 Years Arrives

Philadelphia Weather: Heaviest Snow, Strongest Winds Of Major, Multi-Day Winter Storm On Its Way

MORE NEWS: Philadelphia Area Shops Grateful For Their Regulars On Small Business Saturday: 'That's Our Lifeblood'

‘I’m A Freaking Grad Student’: Philly Fighting COVID CEO Andrei Doroshin Defends Work After City Cuts Ties With Group

Stephanie Stahl