Employees said they have brought it to the attention of their management team, but leaders at work are not giving them answers.
Both local and corporate Chipotle leaders refused to give a statement on the safety of the building.
"Bottom line, this is a horrific accident or worse, a fatality, waiting to happen," said a Chipotle employee who did not want to be identified because they are afraid to lose their job.
"There is a wooden post sticking through the ceiling that is on the ground with a wooden base," said the Chipotle employee.
According to employees, managers said a problem with the ceiling was discovered while repairing another problem inside the Chipotle.
So far, employees have only received excuse after excuse.
"Everything from it's just structural and it's going to be there forever, to it's just a quick fix, and the real fix will come later," said the employee.
The situation has become unsettling for employees who spend hours working inside.
On Tuesday night, employees filed a OSHA complaint.
"Some people are saying they are scared to walk under to get an apron. Others are still unclear of what is happening in the store," said the employee.
Cal-OSHA which works with employees will ultimately send a 'Letter M' to Chipotle. It's a term used in lieu of an inspection letter to speed up the complaint process.
Chipotle did eventually respond on Thursday, and said an engineer noticed a failing beam in the walk-in cooler, and put up a beam to support it for the time being. The engineer was at the location to repair the cooler.
"The wood is breaking. It doesn't look sturdy. It's nothing that is really calming my nerves," said the employee.
Employees said that while the Chipotle doors remain opens, they are afraid to remain inside.
Chipotle's Communications Director, Chris Arnold, sent the following statement to CBS News 8:
While performing equipment maintenance in our restaurant, we discovered what appeared to be a structural issue inside the building where our restaurant is located. Because the safety of our customers and employees is always our highest priority, the space was evacuated and the restaurant remained closed out of an abundance of caution, until a building engineer could assess the issue and repairs could be made. A temporary fix has been made based on the engineer's recommendation and we are working with the landlord and their engineers to be sure the issue is permanently addressed. We appreciate the prompt response from the landlord and the building owner to get this resolved, and will continue to cooperate with them as they work to complete any necessary building repairs.
Employees who are concerned about safety conditions at their workplace can reach out to San Diego's OSHA office.