Balderrama was initially expected to stay in his role pending the outcome of the investigation.
An email from City Manager Georgeanne White to the Fresno Police Department Wednesday afternoon read, in part:
"In light of the intense public scrutiny surrounding the administrative investigation and in the best interest of all parties involved, Chief Paco Balderrama will be placed on paid administrative leave."
It went on to say Deputy Chief Mindy Casto will take over operational control effective immediately.
"Regardless of anything, I'm going to keep doing my job until they tell me otherwise," Balderrama told members of the media in the lobby of City Hall, just hours before being placed on paid administrative leave.
It was the first time he'd spoken publicly since the city announced he's under investigation for an alleged inappropriate relationship.
"This is the most difficult time in my life and in my family's life, so I do ask for a little bit of grace. I do ask for a little bit of forgiveness," said Balderrama.
Balderrama stressed he is not allowed to address the accusations but did point to his work over the past three and a half years of leading the department.
Fresno Police Chief Paco Balderrama speaks on investigation of 'inappropriate' relationship
"I think the police department's work product speaks for itself; you know. My team has done one of the most amazing jobs in the country and I'm extremely proud of them," Balderrama explained.
City officials announced last Thursday that Balderrama told them in February about allegations of an inappropriate off-duty relationship with a non-city employee.
Earlier this week, the chief sent a message to his department asking for forgiveness and saying he owns his mistakes.
Fresno Police Chief Paco Balderrama on paid administrative leave amid relationship investigation
"I do want to say thank you. I want to say thank you to the community and my police officers because I have received hundreds and hundreds and hundreds of messages sending me bible verses, saying that they're praying for me and my family, asking me please don't quit," Balderrama wrote in the message.
The allegations have raised questions and concerns with the Fresno Police Officers' Association.
The union sent out a message to its members Friday, calling the claim by the city that there have been no policy violations "an incredible offense to every sworn member of the agency."
The Fresno Police Officers' Association Board of Directors held a special "executive session" on Wednesday afternoon.
Action News obtained a message sent to members afterward saying the city's decision to place Balderrama on leave is in the best interest of all parties involved.
"We believe this will restore stability to our department after a period of great turmoil," the board wrote in the email.
For news updates, follow Kate Nemarich on Facebook, Twitter and Instagram.
For news updates, follow Nic Garcia on Facebook, Twitter and Instagram.