Gov. Deval Patrick, the third governor to reject Secure Communities, defended his decision to opt out of the controversial federal immigration enforcement initiative on Tuesday by saying it was in the best interest of all of the residents of Massachusetts.

“I made a judgment not on politics, not on how it was going to look, but on the basis of what is best for the whole Commonwealth,” Patrick said at a media roundtable held to address his decision.

Patrick’s office announced Monday that it would not sign the Memorandum of Agreement to participate in the Secure Communities program.

In a June 3 letter sent to Immigration Customs and Enforcement, or ICE, the governor’s public safety secretary, Mary Elizabeth Heffernan, said ICE statistics indicate that only about one in four of those deported since the inception of Boston’s pilot program were convicted of a serious crime and more than half of those deported were identified as non-criminal.

Boston implemented the pilot program in 2006.

Under Secure Communities, once a person is arrested, local police can take their fingerprints and send them to an immigration database maintained by the U.S. Department of Homeland Security. Standard procedure now only includes running fingerprints through an FBI database.

Patrick said that the program has not focused on serious criminal offenders, decreases the willingness of people to cooperate with police, and creates fear in immigrant communities.

The program is slated to be implemented nationwide by 2013.

In May, New York Gov. Andrew Cuomo rejected the program. And before that, Illinois Gov. Pat Quinn told ICE officials that his state would no longer participate. In addition to Illinois, California has also introduced a bill that would allow local communities to opt out of the program.

But Patrick’s rejection of the program will do little to prevent it from being implemented statewide, said a senior Homeland Security official, according to a report in Tuesday’s Boston Globe.

And the decision was condemned by, among others, Republican leaders.

Senate Republican leader Bruce Tarr is backing out on a commitment to the Obama administration, and undoing bipartisan measures agreed upon by the Legislature.

"Hopefully he will address the vacuum he is perpetuating with active and strong support for the practical and substantive measures regarding illegal immigration that were given broad and bipartisan support through Senate actions to include them in the Fiscal Year 2012 budget,” Tarr said in a statement.

Immigrant advocates who have protested the initiative, meanwhile, say that just because the program is federal, it does not prevent local governments or immigrant rights groups from engaging in advocacy to block it from being implemented.

Patricia Montes, executive director of Centro Presente, a statewide advocacy organization, said the group started a campaign called Just Communities last year to pressure Boston to withdraw from the program.

“We don’t need anymore programs that criminalize immigrants,” she said. “There are more than 12 million who live under the shadow…I think the failure not to pass comprehensive immigration reform is a failure of the authorities at the national level.”

Patrick said that if Congress takes up President Obama’s recent outline for comprehensive immigration reform, a lot of the issues being debated surrounding immigration, including programs like Secure Communities, would get solved.

“We have a serious challenge around illegal immigration in this country right now,” Patrick said. “But it is a human issue. It’s about what happens to individuals and families, in many cases, children, who are brought here involuntarily, who are just trying to build the same American Dream that the rest of us aspire to.”

Patrick’s decision comes after months of flip-flopping, during which he said he would not sign onto the program and then changed his mind in December, prompting an outcry from immigrant communities. That outrage led to six community meetings the state held to glean feedback from local residents before officially signing onto the program.

Tanya Pérez-Brennan is a freelance journalist based in Boston. She can be reached at tpb775@yahoo.com.