Janet Daby has relinquished her role as Labour's faith minister after saying that registrars should be allowed to refrain from conducting same-sex wedding ceremonies on religious grounds.
The MP for Lewisham East said last week that there should be a conscientious objection clause protecting registrars from losing their jobs if they refuse to wed a same-sex couple.
"There needs to be something in place that protects people of faith as well as those who think the other way," she said.
"It is an issue of conscience. It is like people having a choice who for reasons of conscience cannot participate in conducting an abortion."
At present, registrars cannot refuse to marry a same-sex couple because of their religious convictions.
Guidance from the Equality and Human Rights Commission, says: "The law is clear that when someone is providing a public service, they cannot, because of their religion or belief, discriminate unlawfully against customers or service users."
Daby announced her resignation on Monday after facing criticism over her comments.
In a statement, she called her comments "misjudged".
"I'm proud to support same-sex marriages," she said.
"On Saturday Labour celebrated 15 years of civil partnerships, and all the progress we've made since. I sincerely apologise for my misjudged comments on Friday, and have decided to resign as Shadow Faith Minister."