Clarence Thomas raised another issue: is Jack Smith legally appointed?

The bulk of the Supreme Court’s decision on executive immunity Monday focused on the charges against former President Donald J. Trump for plotting to subvert the 2020 election.

But a small portion was also relevant to the other federal case Trump faces: the Florida case in which he is accused of illegally retaining a highly sensitive trove of classified documents after he left office and then obstructing efforts to retrieve them.

In a brief concurrence in the immunity opinion, Justice Clarence Thomas said he agreed with the majority’s holding that Mr. Trump enjoyed a substantial degree of protection from criminal prosecution. But he offered his own reasoning for making that decision: He suggested that the special counsel, Jack Smith, who is handling the two federal cases against Mr. Trump, had been given his job without legal basis.

That same question is currently being considered by Judge Aileen M. Cannon, who is presiding over the secret documents case in federal district court in Fort Pierce, Florida. Less than a week ago, Judge Cannon held two days of unusual hearings in Fort Pierce specifically to address the issue of whether Mr. Smith had been properly funded and appointed as special counsel.

Judge Thomas never explicitly mentioned Judge Cannon or the document case in his nine-page concurrence. But he did recommend that “lower courts” consider “the essential questions concerning the appointment of the special counsel” — which is exactly what happened during the hearings in Fort Pierce.

The judge also stated that there would be consequences if Mr Smith was indeed appointed without a legal basis.

“In the absence of a law establishing the office that the special counsel holds, he cannot proceed with this prosecution,” Judge Thomas wrote in what appeared to be a reference to the election interference case, which could easily have a bearing on the secret documents case as well.

“No one can prosecute an ordinary citizen,” he wrote, “let alone a former president.”

Judge Thomas has faced criticism for hearing cases related to Trump, as his wife, Virginia Thomas, better known as Ginni, helped shape the effort to overturn the 2020 election. While Thomas played no role in the secret documents case, evidence has emerged that she pushed hard to keep Trump in office during the chaotic weeks between the last election and the Jan. 6 attack on the Capitol.

In signaling that Mr. Smith’s nomination was in doubt, Judge Thomas adopted Mr. Trump’s position on the issue. In their arguments before Judge Cannon last month, the former president’s lawyers argued that Mr. Smith had not been appointed by the president or confirmed by the Senate, as other federal officials have been.

They also said that Attorney General Merrick B. Garland, who had put Mr. Smith in office, did not have the legal authority to do so on his own.

Mr. Smith’s deputies have countered that under the Constitution’s Appointments Clause, agency heads like Mr. Garland are authorized to appoint “minor officials,” such as special counsel, to act as their subordinates.

In his concurrence, Judge Thomas questioned whether Mr. Smith was in fact a “subordinate officer” and even whether his appointment was valid “unless a statute created the office of special counsel and gave the attorney general the authority to fill it.”

Despite Justice Thomas’ concerns, courts dating back to the early 1970s have repeatedly rejected attempts to challenge the legality of independent prosecutors. These include the Supreme Court upholding the appointment of Leon Jaworski, one of the special prosecutors who investigated the Watergate scandal, in a decision largely focused on President Richard Nixon’s claims of executive privilege.

Judges have also rejected attempts to invalidate the work of special counsel such as Robert S. Mueller III, who investigated ties between Russia and Trump’s 2016 campaign, and David C. Weiss, who brought two criminal cases against Hunter Biden, President Biden’s son.