Video showed protesters inside the church chanting "ICE out" and "Justice for Renee Good", the woman killed by an ICE agent in Minneapolis earlier this month.
Justice department officials, who accuse the protesters of "desecrating a house of worship", say they will investigate them for civil rights violations. President Donald Trump has called them "agitators and insurrectionists".
Anti-ICE protests continue in the state against Trump's immigration crackdown.
Over the weekend, ICE officers arrested a naturalised US citizen at his St Paul home, after breaking down his front door.Videos showed officers escorting Chong Ly Thao, clad only in shorts with a plaid blanket over his shoulders, out of his house with his hands behind his back. Images of the 56-year-old walking to a car in his snow-covered neighbourhood with an ICE agent at each elbow quickly spread across social media.
Thao was returned home later on Sunday.
"I was praying. I was like, God, please help me, I didn't do anything wrong. Why do they do this to me? Without my clothes on," Thao, a Hmong man born in Laos, told Reuters.
The Department of Homeland Security told Reuters that officers were investigating two individuals convicted of sexual offences who were linked to the address. Thao's family told Reuters that one of the individuals of interest previously lived at the address, but had moved out.
The Pentagon has reportedly put 1,500 soldiers on standby for possible deployment.
On Sunday, US Attorney General Pam Bondi vowed to exercise the "full force of federal law" against the demonstrators who interrupted the service at the Cities Church in St Paul, which neighbours Minneapolis.
Later on Monday, Assistant Attorney General Harmeet Dhillon said on X that the justice department "will pursue federal charges in this case".
Protesters say that one of the church's eight pastors, David Easterwood, is a local ICE official.
Easterwood was not leading the service on Sunday.
A person by the same name is identified in ACLU court filings as the acting director of the ICE St Paul field office, according to reporting by the Associated Press and the Minnesota Star Tribune newspaper.
The AP also reported he appeared alongside Department of Homeland Security (DHS) Secretary Kristi Noem in Minneapolis at a news conference last October.
The BBC has contacted the church for comment.
In a statement, DHS said it did not confirm or deny the identities of its agents as "publicizing their identities puts their lives and the lives of their families at serious risk".
Monique Cullars-Doty, a co-founder of Black Lives Matter Minnesota and one of the protest organisers, told CBS News, the BBC's US partner, that "we can't sit back idly and watch people go and be led astray".
In his comments on social media in the early hours of Tuesday, Trump described the actions of protesters at the church as a "raid" that was the work of "professionals".
He went on to write: "They are troublemakers who should be thrown in jail, or thrown out of the Country."
Elsewhere in the city, protests with occasional clashes have persisted at the Whipple building in Minneapolis where federal agents are headquartered.
A DHS spokesperson said on Monday that at least 3,000 people have been arrested in Minneapolis since the deployments.
On Friday, a US federal judge issued an order limiting the crowd control tactics that can be used by ICE agents toward peaceful protesters in Minneapolis.
Thousands of ICE agents are in Minnesota as part of a surge by the Trump administration after his election pledge for the biggest deportation operation of undocumented migrants in history.
On Sunday, CBS News reported that 1,500 active-duty soldiers have been placed on standby for possible deployment to Minneapolis, after President Trump said he may invoke the Insurrection Act to respond to protests.
The 19th-Century law allows the president to use active-duty military personnel to perform law-enforcement duties inside the US.
It was last invoked in 1992 when massive riots broke out in Los Angeles over the acquittal of four white police officers in the beating of Rodney King, a black man.
Separately, the US justice department said on Friday it had opened investigations into Minneapolis Mayor Jacob Frey and Minnesota Governor Tim Walz, both Democrats, for allegedly impeding federal immigration operations.
Both Frey and Walz have spoken out strongly against ICE deployments to their city and state.
Anti-ICE protests have intensified there since the death of Good, a 37-year-old mother of three and a US citizen, who was shot and killed by an ICE agent while in her vehicle in Minneapolis on 7 January.
City officials said she was killed while legally observing ICE activities. The Trump administration, however, labeled her a "domestic terrorist" and said the agent who shot her acted in self-defence.
Meanwhile, an undocumented immigrant has died in custody at an ICE detention centre in Texas, the third such death in 44 days, US media report.
Victor Manuel Diaz, a 36-year-old from Nicaragua, was detained by ICE agents earlier this month in Minneapolis.
"He died of a presumed suicide; however, the official cause of his death remains under investigation," ICE said in a statement.
Earlier this month, a 55-year-old Cuban immigrant, Lunas Campos died at the same facility in Texas.
Tricia McLaughlin, assistant secretary for the Department of Homeland Security, told the Washington Post that Lunas Campos died after attempting to take his own life.