A federal judge ordered Gov. Greg Abbott on Wednesday to move a barrier of floating buoys in the Rio Grande that was placed by the state of Texas to discourage illegal crossings from Mexico, concluding that it was an impediment to navigation on the river and a “threat to human life.”

The Justice Department filed suit in July, arguing that the barrier violated a federal law that prohibits structures in navigable waterways without federal approval.

It said the barrier, placed in a section of the river in the border city of Eagle Pass, Texas, endangered migrants, hampered the operations of the Border Patrol and harmed diplomatic relations with Mexico.

Judge David Ezra of the U.S. District Court in Austin ordered the state to move the roughly 1,000-foot barrier to the U.S. banks of the river by Sept. 15 while the legal case proceeded.

In issuing the preliminary injunction on Wednesday, the judge found that the federal government was likely to prevail on the merits of the case whenever there was a full trial.

The court found that the problems posed by the barrier, which federal authorities said included a risk of drowning by those trying to cross the river, outweighed the interest that Texas had in controlling migration into the state. The judge’s order also halted any new floating barrier construction.

Mr. Abbott’s office issued a statement vowing to appeal the decision. “Texas is prepared to take this fight all the way to the U.S. Supreme Court,” it said. Later on Wednesday, Texas filed a notice of appeal.

The governor, who has pushed the limits of state action on immigration, appeared eager for the court fight over his authority to create a barrier along the border. In a letter to President Biden in July, the governor argued that he had the legal right to do so, in part because of a clause in the U.S. Constitution dealing with state powers during an “invasion.”

The Justice Department, in its lawsuit, focused on what it said was Texas’ violation of a federal law, the Rivers and Harbors Appropriation Act, dealing with federal jurisdiction over navigable waterways. Its lawyers also pushed back on Mr. Abbott’s assertion of a right to declare a migrant “invasion,” arguing that only the federal government could make such a determination.

“Whether and when an ‘invasion’ occurs is a matter of foreign policy and national defense, which the Constitution specifically commits to the federal government,” the Justice Department’s lawyers argued in legal filings.

Judge Ezra said during a hearing last month that he did not intend to broaden the argument over the buoys into a political debate over immigration, saying he was “not here to engage in any kind of political comment in this decision.” He said the question of an invasion was for the political branches to decide, not the courts.

The court fight represented the first direct challenge by the federal government to Mr. Abbott over his increasingly aggressive effort to stop migrants from entering the United States, a sweeping, multibillion dollar program known as Operation Lone Star.

In their response papers, lawyers for Mr. Abbott and the state of Texas argued that the rivers and harbors law did not apply because the Rio Grande in that section was too shallow for navigation, and because the buoy barrier was not physically attached to the riverbed.

They said Texas also had the legal authority to deploy the buoys because illegal crossings by migrants and the smuggling of drugs from Mexico constituted an invasion, which Mr. Abbott had the power, they argued, to declare and combat under the U.S. Constitution, without oversight.

In his decision, Judge Ezra shot down that argument. “Such a claim is breathtaking,” he wrote.

Mr. Abbott has said that the state operation is intended to address the large number of migrants coming to the United States outside lawful ports of entry in the face of what he and other Republicans say is inadequate border enforcement by the Biden administration.

The federal government, in its filings, said the barriers were hazardous for any migrants who might be in distress while trying to cross the river, and also made rescuing them more dangerous for Border Patrol agents. In recent years, according to the filings, there have been 89 water-related deaths of migrants in and around Eagle Pass.

The court agreed that the barrier posed a danger to people, and had negatively affected relations with Mexico. “Credible evidence establishes that the harm from the floating barrier is immediate and ongoing,” the judge found.