Minister Reverend Clay Nelson said the decision to grant sanctuary was "symbolic", and the church would have no power to stop immigration officers if they knocked on the door.
He said the church supported the students in their efforts to finish their courses and year-long work experience. He wanted the Government to find a solution to allow the students to remain on compassionate grounds.
"Supporting justice and fair play is in the DNA of Unitarians. This situation requires a response from us. It is clear that these students are being subjected to a harsh penalty due to the actions of others and not their own. We implore the Government to intercede on their behalf. It is the right thing to do," he said.
In line with church open-door policy, students and their supporters would be welcome in the central city building. He also said there would not be any resistance if immigration officials came to the door.
"Our hope is they won't come knocking and that they'd rather not do that in front of the whole world watching," he said.
"There is not going to be any physical resistance put up. The students are not going to resist."
One student, Asha Rani, and her husband, Vikram Salaria, who are here with their 2-year-old daughter, Khwahish, said deportation would have "a really big impact".
"We don't have any future after deportation. We can't go to any other country. We can't work in a big company [in India] after we get a deportation," Salaria said.
The students say they were not aware that their agents submitted fraudulent documents. The students have paid big fees - $35,000 in Rani's case - to the agents and to the NZ institutions where they studied.
Nelson, a US-born former Anglican priest at St Matthew-in-the-City, said there was a "free-flowing" debate at the Unitarian meeting about "all sorts of other questions about criminal liability and problems with the Building Act".
But he said there was unanimous support in the end for two resolutions - one supporting the students and asking the Government for compassionate relief, and one reaffirming the church's "open-door" policy.
"Churches have had a long history of providing sanctuary, even though it has no standing in law either here or in my home country," he said.
"It's part of their mission, that they feel called to support 'the least of those' in terms of our society."
Nelson compared the students with Muslims and refugees who were caught in President Donald Trump's proposed 90-day ban on entry to the United States.
"I am really struggling with what's happening in my home country and grateful for the support of cities and people on the women's march and those going to airports to protest the ban," he said.
"It's only by that kind of civil action working collectively that we are going to be able to resist what I think are some pretty evil days ahead."
A spokeswoman for Woodhouse said on Friday that the minister did not personally decide not to intervene in the students' case, but left it to his officials.
"It didn't come across his desk," she said. "This is not a unique situation in that delegated decision makers have made the decision."
