Missouri health officials on Friday refused to renew the St. Louis clinic's license on the grounds that it failed to meet their standards.
But Circuit Court Judge Michael Stelzer last week left in place an injunction blocking its closure.
On Monday, Stelzer ruled the clinic can stay open until Friday but ruled that the case must go before the Administrative Hearing Commission, which serves as an independent arbiter in disputes between state agencies and individuals or groups.
If Missouri officials succeed in closing the clinic, the state would become the only U.S. state without a legal abortion facility.
Abortion is one of the most divisive issues in the United States. Missouri is one of 12 states to pass laws restricting abortion access this year, some aimed at provoking a U.S. Supreme Court review of the landmark 1973 Roe v. Wade decision that recognized a woman's constitutional right to terminate her pregnancy.
The legal battle in Missouri over the fate of the clinic, which is called Reproductive Health Services of Planned Parenthood, began on May 24 when Missouri's Republican governor, Mike Parson, signed a bill banning abortion beginning in the eighth week of pregnancy.
Stelzer ruled Planned Parenthood, the national women's healthcare and abortion provider, had failed to exhaust its remedies before administrative officials and that, as a result, the case should not be heard in state court. The clinic will have to shut its doors if the commission does not act before the end of business on Friday, Planned Parenthood said in a statement.
"The terrifying reality is that access is hanging on by a thread with a narrowing timeline," Dr. Colleen McNicholas, a physician at the clinic, said in a statement provided by Planned Parenthood.
A representative for Parson declined to immediately comment on the judge's latest ruling.
State officials have said one of their conditions for renewing the clinic's license was to be allowed to interview several physicians who were involved in what they said were multiple life-threatening abortions at the clinic.Planned Parenthood officials have said they do not directly employ all the clinic's staff and cannot force certain health workers to give interviews.