A federal judge ruled Tuesday that Missouri should use a new congressional map that favors Republicans for now, hours after the U.S. Supreme Court left in place a ruling from the state’s highest court directing Missouri to use an older map.

The Supreme Court rebuffed an appeal from Missouri officials who wanted to use new congressional districts backed by President Trump in the November election, marking a defeat for Republicans who had hoped the new map could help them hold on to their slim House majority. The justices let stand a decision by Missouri’s top court, which said the new districts cannot be used in the November elections because they were superseded by a citizen petition demanding a statewide vote.

But shortly after, U.S. District Judge Stephen Clark issued a temporary restraining order in a separate challenge to Missouri’s Supreme Court decision, writing that the plaintiffs faced “irreparable harm” otherwise because “many Missouri voters would have to cast their general-election votes for candidates whom they had no role in nominating.” 

The decision adds further confusion about which boundaries will be used in November. 

The new House maps, passed by the state legislature last year, would dramatically redraw longtime Democratic Rep. Emanuel Cleaver’s Kansas City-area district, making it GOP-leaning.

Missouri’s new districts were used in the August primaries. But the Missouri Supreme Court ruled last week that the state must revert to districts adopted after the last census.

Republican state Attorney General Catherine Hanaway, who appealed to the U.S. Supreme Court, had argued it would violate federal rights to switch districts for voters between the primary and general elections. She also said it would cause confusion.

“A federal-election-administration disaster is unfolding in Missouri,” Hanaway wrote in an emergency application for the U.S. Supreme Court to put the ruling on hold, warning it could lead to “unprecedented chaos” and render the primary “utterly pointless.”

She continued: “Looking forwards, the State is genuinely unsure whether it can switch its governing congressional map in time to run a timely federal election.”

Richard Von Glahn, who sued over the new maps, urged the U.S. Supreme Court not to intervene, writing that the state “waited as long as possible to manufacture the present dispute over Missouri’s congressional districting map” by not moving to reject the petition for a referendum until last month.

Hanaway’s request for the U.S. Supreme Court to step in was rejected by Justice Brett Kavanaugh on Tuesday.

Missouri currently is represented in the House by six Republicans and two Democrats who were elected under districts that Republican state officials approved in 2022.

But at Mr. Trump’s urging, Missouri Gov. Mike Kehoe called the Legislature into a special session last year to redraw congressional boundaries to their advantage ahead of the midterms.

The revised map targeted the 5th Congressional District, held by Cleaver. It reassigned portions of Kansas City to two neighboring districts represented by Republicans and stretched the remainder of Cleaver’s district far eastward into rural Republican areas.

Cleaver was unopposed in the Democratic primary. State Sen. Rick Brattin won the Republican primary in the reshaped district.

On the same day as the primary, Republican Secretary of State Denny Hoskins rejected a petition with thousands of signatures seeking to force a November referendum on the map. Hoskins asserted that Missouri’s Constitution doesn’t allow a referendum on congressional redistricting. A lower court agreed, but the state Supreme Court reversed Hoskins’ decision.

The state’s top court said the new districts were retroactively frozen in December, when the petition signatures were submitted, and thus never became law. Hoskins on Tuesday assigned the redistricting referendum as Proposition A on the November ballot, in compliance with the state court order.

The Missouri Constitution does not specifically say that a referendum can be used for congressional redistricting. But the state Supreme Court said a constitutional provision allowing a referendum on “any act” of the Legislature encompasses congressional redistricting legislation.

Missouri was the second Republican-led state, after Texas, to respond to Mr. Trump’s call last year to redraw congressional districts. Several other states followed. All told, Republicans had hoped to win as many as 16 additional seats from new House maps enacted in eight states — Texas, Missouri, North Carolina, Ohio, Florida, Tennessee, Louisiana and Alabama. 

Democrats, whose counterattack faced several setbacks, think they could win up to six additional seats from new districts in California and Utah.

It remains to be seen whether the redistricting works as intended for Republicans. The president’s party historically has lost congressional seats in the midterms, and Mr. Trump’s poor approval ratings could provide an extra hurdle for Republican candidates.