The clinic will remain open and operational until the court-ordered temporary restraining order is withdrawn or ended by the court.
The health department was ordered to make a decision about the facility's license by June 21.
Randall Williams, the director of DHSS, said the decision was based on the fact that of 30 deficiencies found in the department's review of the clinic, only four have since been addressed by Planned Parenthood.
He did not list all 30 deficiencies, but gave reported examples that included an instance where the doctor who performed the pre-operative review of the patient was not the one to perform the surgery itself, which goes against state laws. He also gave reported examples of two patients who had failed abortions and had to have multiple procedures.
Williams was asked if the denial of their license was influenced by political pressure, and he said "absolutely not."
"In the regulatory environment, our north star is always the individual," he said, adding, "We never let anything interfere with the basic patient care that a patient is receiving."
In Planned Parenthood's statement, issued before Williams' remarks, they slammed the move as being impacted by the state's Republican governor, who recently passed a ban on abortions after eight weeks into a pregnancy. That law is currently being challenged in a separate court battle and has not gone into effect.
"While Gov. Parson and his political cronies are on the wrong side of history, nothing changes right now for patients who need access to abortion at Planned Parenthood. We will continue providing abortion care for as long as the court protects our ability to do so," Dr. Colleen McNicholas, an OBGYN who works at the clinic, said in a statement released Friday.
One of the points of conflict between health department administrators and clinic doctors was the implementation of a pelvic exam, which the state required but doctors felt was unnecessary and potentially triggering.
While the clinic's doctors said previously that they reluctantly performed those exams in keeping with the law, on Wednesday one of the clinic's doctors announced they will no longer be performing the exams.
If the court revokes the restraining order, the clinic will close, making Missouri the first state without an abortion clinic.