Citizenship lists that the Trump administration has ordered be compiled and shared with state election officials this year are likely to be incomplete and unreliable for determining voter eligibility, the Justice Department told a federal judge on Thursday.

The admission, in Federal District Court in Washington, came in a lawsuit challenging an executive order President Trump signed in March that would create state registries of citizens using federal data, and require the U.S. Postal Service to regulate mail-in voting.

The admission appeared to compound what Mr. Trump had already acknowledged could be legal troubles for the order, which is part of his sweeping attempt to bend election mechanics to his will. The Constitution does not give the president any explicit authority over elections, and Democratic-led states and organizations are turning to the courts to try to halt the efforts.

During the hearing on Thursday, Stephen M. Pezzi, a senior counsel at the Justice Department, told Judge Carl J. Nichols that it was too speculative to anticipate that states might seize on the lists to purge registered voters.

“No list is ever going to be perfect,” he said. “Certainly, a responsible state wouldn’t throw everyone who isn’t on the list off the voter roll.”

Mr. Pezzi allowed that it was possible that some states might be “overzealous” in checking the lists against their current registered voters, after Texas last year compared its voter rolls with federal data and started the process of removing roughly 2,700 voters deemed “potential noncitizens.”