The Department of Homeland Security conducted an early morning raid of undocumented immigrants in New Haven on Wednesday, arresting dozens and prompting city officials to decry what they believe to be federal retaliation for the city’s approval Monday of the first-in-the-nation municipal ID program.

Immigration and Customs Enforcement agents made 29 arrests Wednesday, according to a spokeswoman for the agency, and city officials said they expect more arrests over the course of the next two weeks. The officials described it as the first-ever mass arrest of illegal immigrants in recent New Haven history, but the ICE spokeswoman says the arrests are not politically driven and are “routine.”

New Haven Mayor John DeStefano Jr., who will be holding a press conference to discuss the arrests later this afternoon, says the federal government arbitrarily targeted New Haven immigrants in response to the Board of Aldermen’s approval of municipal ID cards. The ID cards will be available to all city residents, regardless of their citizenship status, and will allow cardholders to access basic city services and protections.

“We feel that this is too much to be a coincidence, this is a retaliation,” said Jessica Mayorga, DeStefano’s spokeswoman, who called the events a “very big surprise.” “They are attacking us because they failed to integrate immigration reform that worked. That’s not our fault, and we’re doing everything we can to protect the immigrants of New Haven.”

Mayorga said the mayor has not yet devised a response to the events, as the more immediately pressing concern now is the children who will come home to find that their parents have been arrested. Those detained will likely be sent out of state, and a team from Yale Law School has already agreed to represent them.

But Paula Grenier, a spokeswoman for the federal Immigration and Customs Enforcement Office, said Wednesday’s arrests were nothing out of the ordinary, and she denied any connection between the approval of the ID program and the raids.

“Our Fugitive Operations Team was out today and in New Haven and did make some arrests, but again these are specific arrests,” she said, adding that there are over 20,000 such arrests made throughout the country each year.

She said she did not have records available as to when the last arrest was made in New Haven.

During discussions of the ID program, aldermen expressed some concern that the Department of Homeland Security at some point might subpoena the program’s records, but there was little if any discussion of a possible retaliation by immigration enforcement, especially before the ID cards were put into place.

Ward 1 Alderman Nick Shalek said “everybody is very surprised” by the arrests, which took place in the Fair Haven neighborhood.

“I’m still in favor of the Municipal ID program and practical efforts to make the city a safer place for all its residents, undocumented and otherwise,” Shalek said. “To the extent the raids are in retaliation to the city’s actions, I am severely disappointed and distraught.”

Shalek said he has received dozens of e-mails from students in what he called the largest outpouring of student interest in a political issue that he has witnessed as an alderman.

The ID program was approved Monday by a vote of 25-1, with the dissent coming from the only Republican on the Board, Ward 18 Alderwoman Arlene DePino. Hundreds of undocumented immigrants have descended on City Hall in recent weeks to show their support for the card program. But many aldermen have said that they have also received a barrage of e-mails decrying the plan as a deliberate circumvention of federal law.

Board of Aldermen President Carl Goldfield could not be reached for comment Wednesday afternoon.