A key immigration enforcement program that has drawn criticism from some state and local governments will terminate all existing agreements with jurisdictions over the program, federal authorities announced Friday.

Immigration and Customs Enforcement said its director, John Morton, had sent a letter to state governors terminating the agreements “to avoid further confusion.”

Through the program, the FBI shares fingerprint data of people arrested by local and state law enforcement agencies with federal authorities, who can use the information to check for immigration law violations. The agreements were meant to educate states about the availability of the service, ICE officials say.

The initiative, which began in 2008, has been implemented in about half the jurisdictions in the country, with a goal of having it in place nationwide by 2013.

Inconsistent federal guidelines on the program have created confusion, with some jurisdictions, such as Arlington County, forced to participate against their will while others, such as the District and Montgomery County, have been given more latitude.

Although the program, called Secure Communities, was initially widely thought to be voluntary, federal officials have since said that there is no room for local jurisdictions to opt out. The memoranda of agreement, which states signed under the previous administration, may have given a false impression that participation was optional.

“Today’s action represents a disagreement with that approach, and we’re trying to put more clarity into how this system actually works,” a Department of Homeland Security official said Friday. “We’re going to continue the program, but we’re going to do it without MoAs.”

Immigrant advocacy organizations responded angrily to the announcement. “For DHS to act with such disregard for local leadership, community policing and fiscal prudence is an act of bad faith and bad policy,” Ali Noorani, executive director of the Washington-based National Immigration Forum, said in a statement.

Immigrant advocates have criticized the program, saying that it does not distinguish enough between minor offenders and serious criminals. They say it could discourage victims and witnesses from reporting crimes for fear of being swept up in arrests and tagged for deportation.

In June, the government announced measures designed to offer greater protection to crime victims and witnesses.