The complaint says the Trump administration’s practice of separating families at the border would be considered “child abuse” under church law.

Stories of children being taken from their parents and images of teenagers in cage-like detention facilities have turned into a crisis for the Trump administration, which announced plans on Wednesday to end the practice of family separation in illegal immigration cases. Families would be detained together indefinitely under the expected order, which could run afoul of a 20-day legal limit on how long children can be kept in detention.

Last week, as the opposition was building, Mr. Sessions used a Bible passage to defend the “zero tolerance” policy, in a speech to law enforcement officers.

Now he faces a complaint from within his own church, sent this week to his pastors in Alabama and Virginia.

The formal notice starts a process that could in theory ultimately lead to Mr. Sessions’s termination from the church, though such an outcome would be extremely unlikely.

Instead, the complaint seeks a “a reconciling process” that would prompt Mr. Sessions to “step back from his harmful actions and work to repair the damage he is currently causing to immigrants, particularly children and families.”

“He is ours, and we are his,” the letter, signed by 639 individual Methodists, including clergy members, reads. “As his denomination, we have an ethical obligation to speak boldly when one of our members is engaged in causing significant harm in matters contrary to the Discipline on the global stage.”

The Justice Department did not immediately answer a request to respond to the complaint.

Mr. Sessions’s Alabama pastor, the Rev. Sterling Boykin, did not respond to a request for comment. Nor did his Virginia pastor, Tracy Wines.

The complaint was just the latest example of how widespread criticism of the family separations has been. Congressional Republicans had moved to end the practice. Conservative religious leaders voiced opposition. The four living former first ladies condemned the policy, and even Melania Trump, the current one, seemed critical of the practice in a statement.

This week’s complaint from 639 members of the United Methodist Church states that they were “reticent” to bring the complaint against Mr. Sessions, but that it was necessitated by his leadership roles inside the church, including as a Sunday school teacher.

It outlines four “chargeable offenses” against Mr. Sessions as prescribed by Methodist church law.

In addition to “child abuse,” the complaint also seeks charges of “immorality” for the separations, “racial discrimination” for indicating that the federal government would back away from monitoring troubled police departments, and “Dissemination of doctrines contrary to the standards of doctrine of the United Methodist Church” after Mr. Sessions used the Bible to defend the zero tolerance policy.

The United Methodist Church has more than seven million members in the United States and more than 44,000 clergy members.

The Rev. William B. Lawrence, a professor emeritus of American church history at Southern Methodist University’s Perkins School of Theology and ordained minister in the United Methodist Church, said complaints are treated the same by the church whether filed by one individual or hundreds. Mr. Lawrence said complaints are filed regularly.

He said it was significant that many members of the church from across the country had signed on to the complaint against Mr. Sessions, which included people from California, Florida, Texas, Illinois, Washington and other states.

Mr. Lawrence said though the complaint process could lead to termination of Mr. Sessions’s membership, the church is “so many steps removed from that hypothetical outcome.”

First, a pastor or another local church leader may attempt to resolve the complaint. Mr. Lawrence said that could be done by having a conversation with the individuals behind the complaint and with Mr. Sessions, though pastors have wide flexibility.

There is no timeline outlined in church law governing how fast they must act, though they are required to respond in some way, Mr. Lawrence said.

If a resolution is not successful, a committee could be appointed to investigate, and eventually the church could hold a trial that could eventually lead to termination.

A spokeswoman for the United Methodist Church’s Alabama-West Florida Conference, a body that includes Mr. Sessions’s Alabama church, said that the conference had received the complaint and that the church would be following disciplinary protocol, but declined to comment further, stating that the procedures are confidential.

Since the United Methodist Church was created in 1968, Mr. Lawrence, who has been an ordained minister for 49 years, said he had never seen a complaint that was not resolved by a pastor or other local church leader.