Immigration and Customs Enforcement officials sent e-mails to government and police officials in those states saying the program, Secure Communities, would be activated "in all remaining jurisdictions" Tuesday.
Plans to extend the controversial program, which has been in place in Boston since 2006, were shot down by Massachusetts Gov. Deval Patrick last June, and New York Gov. Andrew Cuomo said he wanted to suspend the program in his state, The New York Times reported.
However, both governors were overruled by federal officials who mandated the program be extended.
"Secure Communities has proven to be the single most valuable tool in allowing the agency to eliminate the ad hoc approach of the past and focus on criminal aliens and repeat immigration law violators," Barbara Gonzalez, a spokeswoman for ICE, said Friday.
Under Secure Communities, fingerprints from anyone booked for any offense are sent through the FBI databases of the Department of Homeland Security, which include immigration records. If there is a match ICE then decides whether to deport the individual.
Last year, the immigration agency decided it does not need the states' permission to go ahead with the program. Citing anti-terrorism legislation Congress passed in 2002, agency officials said they would activate the program nationwide by 2013.
"At the end of the day, this is a federal program," a Department of Homeland Security official said. "We have to make our own decisions based on our law enforcement operational needs."
Opponents of the program argue it is used to deport undocumented immigrants with no criminal histories who were arrested for minor offenses. They also say it encourages racial profiling.
Boston Mayor Thomas Menino spoke out against the program in an interview Friday, saying, "It's dangerous to target immigrants when you are trying to build a community.
"The information gets put into a computer and sent to Washington and the wrong person gets deported," he said. "I want to make this city work and to have the feds come in and tell me you have to do this or to do that is just wrong."