Washington (CNN) A federal judge paved the way Tuesday for possible future subpoenas by the State Department against Hillary Clinton and her longtime aide Huma Abedin.

Judge Emmet Sullivan granted a motion in a lawsuit against the State Department Tuesday that could pave the way for future action including, potentially, an order that the State Department subpoena Clinton and top aide Huma Abedin to obtain personal emails they withheld from the State Department.

The case is seeking answers to lingering questions about Hillary Clinton's use of a private email server during her time as secretary of state.

Sullivan appeared at times to be leaning towards ordering the subpoenas, but ultimately said he would wait to see what the order for discovery yields before making that ruling.

"This is the atypical case," Sullivan said, who emphasized earlier in the hearing that discovery is rare in Freedom of Information Act (FOIA) cases, which pertain to information requests to the government.

On Tuesday, the judge ruled that discovery was warranted in this case because Clinton's exclusive use of a private email server to conduct official business was condoned by the State Department, which tacitly allowed her keep those records when she left office.

Judicial Watch, a conservative group that filed the lawsuit, must now submit a discovery plan to the court within three weeks, after which the State Department will have three weeks to respond.

In a statement after the hearing, Judicial Watch President Tom Fitton said they would seek testimony from current and former State Department officials as part of their discovery plan.

"While Mrs. Clinton's testimony may not be required initially, it may happen that her testimony is necessary for the court to resolve the legal issues about her unprecedented email practices," Fitton said.

Clinton's use of the server was first revealed by a New York Times report last March, two years after she left office, and a few months after the State Department asked her to return any official emails.

Abedin, who was Clinton's deputy chief of staff at the State Department and is now a top official on her presidential campaign, also used an email account on the private clintonemail.com server.

This particular case -- one of a number filed by conservative groups about Clinton's time as secretary of state --was originally filed by the private watchdog group Judicial Watch in 2013 over a document request related to Abedin was allowed her to simultaneously work for a foundation run by the Clintons and a private firm, while still consulting with the State Department.

It was settled shortly after by the parties, but revived amid the revelation of Clinton and Abedin's email practices, which prevented the bulk of their emails from being searched for responsive records by State Department FOIA personnel.

The issue of whether State should seek the emails Clinton's team determined to be personal is "an issue worthy of discussion at the appropriate time," Sullivan said, bemoaning at one point the resources that have been spent by all parties as a result of Clinton's decision to use a personal email server.

"It just boggles the mind a little that the State Department allowed this practice to occur in the first place," said Sullivan. "It is very, very troubling."

Sullivan said he would "give (the subpoena issue) some thought," and hopes the State Department's response, due in April, will put the court in a better position to determine whether the State Department has taken adequate steps to obtain an search official records.

Last year, Sullivan ordered the State Department to seek declarations from Clinton and Abedin asserting they had turned over relevant documents, and asked the State Department to coordinate with the FBI, which now has possession of the email server, in finding other potentially relevant records.

Clinton, Abedin and the FBI are not party to the lawsuit, so Sullivan could not issue orders to them directly.

Sullivan said he was pleased with the State Department's compliance on these steps, but said questions remain as to why the private system was set up in the first place, and whether it was, as Judicial Watch asserts, an attempt to thwart the FOIA process.

"This is a public forum," said Sullivan. "This is about the public's right to know."

Steven Myers, an attorney for the State Department, argued at Tuesday's hearing that the agency has already conducted a reasonable search for records, having obtained nearly 55,000 pages of official emails from Clinton, which they are releasing to the public under a time line set in a separate FOIA case.

Furthermore, Myers argued, the State Department should not be expected to search records they don't physically possess.

It is unclear whether Clinton and Abedin's attorneys still have copies of the emails in question, having turned the server's contents over to the FBI last year.

The FBI is conducting its own investigation into the set-up of the server.