SPRINGFIELD — The coffee in the pot was still warm Thursday morning as city officials began inspecting the second-floor apartment inside South Congregational Church where a Peruvian immigrant is being sheltered from deportation.

The stated reason for the inspection was to make sure the apartment where Gisella Collazo and her two children have been living for the past two weeks meets health and safety standards. But immigrant advocates and some city councilors see a more sinister motive — a direct threat to the immigrant sanctuary movement.

In June, when the church announced it would join the sanctuary movement, becoming a place of refuge for people fleeing immigration authorities, the city said in a statement that Mayor Domenic Sarno would “not stand for harboring and protecting’’ immigrants facing deportation, and that the church wasn’t “designed to be safely occupied as a housing shelter.’’

The mayor is the only official in Massachusetts to challenge a church offering sanctuary.

Last week, Sarno ordered the church inspected for “illegal housing’’ and directed city officials to start the process of stripping it of its tax exempt status.

Christine Tetreault, the church’s attorney, refused this week to allow city officials entry unless they had a warrant.

And so, at about 9 a.m. Thursday, Code Enforcement Commissioner Steve Desilets and Lieutenant Richard Martin with the Springfield fire marshal’s office walked up the church stairs and into the tidy two-bedroom apartment, making good on a promise to return with a warrant.

What did they find?

Neatly made beds. Towels hung from hooks in a wardrobe where tiny pairs of sneakers were lined up underneath.

Working smoke detectors. Sufficient entrances and exits. But they discovered windows that need fixing. A broken door lock. And a table blocking a door.

“Just minor issues,’’ Desilets said. “Minor violations that probably can be fixed by the end of the afternoon.’’

Desilets said they were not there because of Collazo’s immigration status, or because of the spat between the mayor and the church.

“It doesn’t matter if it was an immigrant family or the pastor’s family, our intention was never to kick anybody out,’’ Desilets said. “It was whether or not it met minimum standards.’’

Some, however, are dubious about that claim.

City Councilor Adam Gomez, who was at the church Thursday morning, said the city has plenty of dilapidated and blighted buildings that need attention more than the church.

“This, right here, you’re attacking a church,’’ he said, adding that he supports a proposed order by a fellow councilor to bar any city official from interfering with the church’s sanctuary effort. “We could use those resources on other buildings, other blighted property that are really run down and making our community look deplorable.’’

As officials conducted their room-by-room inspection, the Rev. Liza Neal, director of spiritual life at Hampshire College, asked about a dozen clergy members from several churches gathered in the hallway to clasp hands and bow their heads in prayer.

“Holy God, be with us this morning,’’ she began. “We thank you for Gisella, her children, her husband, for all those here throughout this church, throughout this community, this city, this state, this country who are praying desperately for kindness, for hospitality, for justice.’’

Collazo and her children have lived at the church for less than two weeks. Collazo emigrated from Peru in 2001 and married a US citizen four years later.

Her children were born in the United States.

In 2006, she received a work permit and began the process to become a citizen, but mistakes were made along the way, and during her Jan. 29 check-in with immigration officials, she was told to return with a ticket to Peru on March 26. Instead, she sought sanctuary inside of South Congregational.

The church and a consortium of community groups, including the Springfield Interfaith Sanctuary Coalition, which is part of the Pioneer Valley Project, informed immigration officials that Collazo was seeking sanctuary at the church.

During the inspection, Martin climbed a ladder and tested the living room smoke detector, which blared “Warning! Evacuate!’’ as the pastors in the hallway began singing the Latin hymn “Ubi Caritas.’’ Over and over, they sang in Latin: “Where charity and love are, God is.’’

Collazo missed all of this. She was sequestered in another part of the church Thursday, and the children were at school.

“No one wants to be in sanctuary. It’s glorified house arrest,’’ said Louis Mitchell, the church’s assistant minister. “She’s left her job. Her husband is having health problems behind this. The kids came with her because they were freaking out.’’

Mitchell said the decision to shelter immigrants is a result of President Trump’s crackdown on illegal and legal immigration. But the concept of churches providing sanctuary to immigrants facing deportation goes back decades. And while churches cannot legally protect immigrants from deportation, immigration authorities have generally not taken people into custody in houses of worship, schools, or hospitals.

Sarno said last week in a statement that he was “disappointed’’ that the church would “exploit this family.’’

“Now, I’m not a cold-hearted person and do have compassion for the family in question,’’ he said, “but there must be a clear path to American citizenship, whether it’s this case in Springfield or in other parts of our country.’’

As for Thursday’s inspection, Sarno said in a statement that inspectors “have done their jobs and their report speaks for itself.’’

Church officials said they will not be deterred.

“No regrets,’’ Mitchell said. “For us, being a host is what we do. Serving is what we do. We’re a church. Give your prayers and energy to Gisella and her family.’’

Akilah Johnson can be reached at akilah.johnson@globe.com. Follow her on Twitter @akjohnson1922.