Missouri's health department will not renew Planned Parenthood of St. Louis's license to perform abortions, according to a letter from the state's health department provided to CBS News. However, a district judge will allow the clinic to continue to perform abortions, for now.

In late May, the clinic sued the state for "refusing to renew" its license, which was set to expire on May 31. A district judge granted Planned Parenthood a preliminary injunction, allowing the clinic to continue providing the procedure, until the state made a final ruling on the license. The state's deadline to make that decision was today.

In court on Friday, Judge Michael Stelzer allowed the preliminary injunction to stand until he made a final decision on what would happen next with the clinic. The judge called the case one of the most difficult of his career.

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Now, the judge will decide whether the license battle will stay within the jurisdiction of the court, or head to an administrative hearing.

A letter to Planned Parenthood from the Missouri Department of Health and Senior Services claimed there were "deficiencies" at the clinic and a failure to correct them. "The Department therefore denies RHS' application for a license renewal," the letter says, referring to the Reproductive Health Services division of Planned Parenthood.

"Missouri Gov. Mike Parson's Department of Health and Senior Services (DHSS) weaponized a regulatory process to deny an abortion facility license to the last remaining health center in Missouri that provides abortion," Planned Parenthood said in a statement. "The fate of abortion access in Missouri now rests in a court's hands."

Dr. Leana Wen, president of the Planned Parenthood Federation of America, told CBS News' Dr. Jon LaPook, "Once again, we came within hours of having more than a million women in Missouri not have any place to go for reproductive health care — which is health care. This is the state of emergency that we have all across the country."

She added, "We have a temporary reprieve, but this is only temporary."

The latest development follows weeks of back-and-forth with state health officials.

On May 20, Missouri's health department notified Planned Parenthood of issues that could impact license renewal, and Planned Parenthood agreed to address some of them, including a request to perform two pelvic exams.

But this week, Planned Parenthood doctors said they would conduct a pelvic exam only at the time of the procedure — which is when they deem it medically relevant — not at the initial consultation 72 hours prior. They called the requirement for a second pelvic exam "unethical."

In a statement Friday, Governor Mike Parson said, "If you don't comply with the law, there will be consequences. If you don't provide a standard of care that ensures the safety of women, you shouldn't be allowed to operate."

Missouri is one of six states with only one abortion clinic. Planned Parenthood would still be able to provide non-abortion health services for women in Missouri.