A video shot inside the Allen Chapel African Methodist Episcopal Church showed a Pensacola police officer stopping the service to try and give the court order to a member of the congregation over a child custody issue.
The video has received more than 300,000 views on Facebook and has sparked hundreds of comments over the action of the policewoman.
But Pensacola Police Chief David Alexander III says the officer involved, Officer Meghan Darling, acted within her duties while inside the church.
She stopped the service as the congregation was preparing to take Communion.
Speaking to USA Today he said: "Officer Darling went over to the church with the father of the child, hoping to mediate a peaceful exchange for the child, who was with her grandparents," Alexander said.
It is thought the child involved lives with her grandparents, not her father.
The 13-year-old girl was with the Revd Freddie Tellis, who was conducting the service, was inside the church with his wife at the time the officer entered.
USA Today has reported that after a number of attempts to enact the custody court order with deputies from the Escambia County Sheriff's Office at the grandparents' home, her father discussed the failure to return the child to him with police.
The child was later located at the AME church and the father and officer Darling travelled there in the hope of completing a custody order.
Police Chief Alexander added that: "The officer was questioned several times by members of the church - and continued to wait for the pastor."
Other members of the church filmed the exchange between the officer and Revd Freddie Tellis, who asked her to leave.
He said: "I respect that they have a job to do, but the way they went about it was wrong.
"The police had no authority to violate the sanctity of a worship service."
He added: "I respect the law, but you have to respect people's religious freedom - I think it could have been handled differently."
According to the police, any church that is incorporated within the State is technically public space.
Police Chief Alexander said: "We certainly respect the fact that it's a church, but we also respect the fact that lots of times we have to respond to churches because there are problems.
"(The father) asked for help today and we were trying to resolve this thing in the most peaceful way possible.
"The pastor was aware of the court order and at some point had communicated that if the officers came for the child, he would surrender the child.
"However, that did not take place, and this turned out to be a long, drawn-out issue between him and his son-in-law."
Officer Darling's supervisor joined her shortly after her first attempt to contact the grandparents inside the church and it was agreed the child could stay for Communion before leaving with her father.
The daughter was placed in the custody of her father and left the church with him after the service.
