A federal judge on Long Island chided the Justice Department on Wednesday for trying to “avoid public scrutiny” of its attempts to drop criminal charges against a high-ranking member of the violent street gang MS-13 and quickly deport him to El Salvador, his homeland.

In April, federal prosecutors had asked the judge, Joan M. Azrack, to allow them to dismiss the charges against the MS-13 leader, Vladimir Arévalo Chávez, under seal and to keep the entire matter secret until he was returned to El Salvador.

The Justice Department is seeking to deport Mr. Arévalo in the wake of a deal that President Trump reached with Nayib Bukele, the Salvadoran president, who had agreed to use his country’s prisons to house hundreds of immigrants that Trump officials were looking to expel from the United States.

The United States not only agreed to pay millions of dollars to El Salvador to help Mr. Trump carry out his deportation agenda, but also added an important sweetener at Mr. Bukele’s request: the return of key MS-13 leaders, like Mr. Arévalo, who were in American custody.

Judge Azrack ultimately rejected the government’s request to keep the effort to dismiss Mr. Arévalo’s case secret, and unsealed the paperwork in May. In a 29-page opinion issued on Wednesday, she explained why she had revealed the behind-the-scenes move. While the Justice Department had publicly celebrated its charges against some MS-13 leaders as “swift American justice,” she said, it was also throwing out the case against Mr. Arévalo.

“The government appears to be making inconsistent representations,” she wrote, “and the public has a right to know about this motion before its resolution.”