Church spokesman John Coleman said that officials decided to defrock him.
Schaefer left the short meeting with church officials without commenting but planned to address the matter later Thursday.
Earlier this week, Schaefer said he would defy the religious order to surrender his credentials for performing the same-sex wedding.
Schaefer was told to give up his pulpit in central Pennsylvania by Thursday if he cannot support the denomination's Book of Discipline. But Schaefer, who describes the book as contradictory and biased against gay people, said he will not go quietly.
"I am actively committing to having those discriminatory laws changed and banished from our Book of Discipline," Schaefer said. "That's the only way I can reconcile being a United Methodist at this point."
Schaefer was serving a 30-day suspension for officiating the 2007 wedding of his gay son in Massachusetts, where same-sex unions are legal. Although the Methodist church accepts gay and lesbian members, it rejects the practice of homosexuality as "incompatible with Christian teaching."
Jurors who convicted Schaefer in a church trial last month said he should use the suspension time to decide whether he could follow church doctrine. They ordered him to resign from the clergy if he could not.
Schaefer gave his answer publicly Monday during a news conference at Arch Street United Methodist Church in Philadelphia, surrounded by dozens of sympathetic ministers and laity.
"I cannot voluntarily surrender my credentials because I am a voice now for many — for tens of thousands — of LGBT members in our church," he said then.