"I think we all have concerns for those who are caught in this trap through no fault of their own and are here," Boehner said in his first public reaction to the policy announced Friday.
The Obama administration's directive will specifically allow people younger than 30 who came to the United States before age 16, pose no criminal or security threat and were successful students or served in the military to apply for a two-year deferral from deportation.
Top GOP leaders were caught off guard by the announcement, and stayed quiet on the issue. Republican aides acknowledge immigration is a divisive issue within their party and those GOP members in competitive districts need to appeal to Hispanic voters to win re-election this fall.
But many conservative House Republicans immediately blasted the decision last week, and Iowa Republican Rep Steve King announced he planned to sue the Obama Administration.
A Bloomberg poll released on Tuesday shows that 64% of voters support the policy, with independent voters backing the change by a 2-1 margin.
Boehner blamed the President for not working with Congress, saying he didn't consult with the GOP before making his announcement. "The President's actions make it much more difficult for us to work on a bipartisan way to get to a permanent solution."
Noting that the President himself said previously that he couldn't act on the matter, Boehner told reporters Tuesday, "the question remains, did he violate the Constitution?"
Boehner repeated his criticism that the President doesn't want to talk about the economy "so he's turned to the politics of envy and division, which I don't think the American people are going to accept."
Even though Boehner recently admitted it would be "difficult at best" to pass any immigration legislation in this Congress, he said there need to be reforms.
"We've got to do a comprehensive immigration reform plan that secures our borders, enforced our laws and fixes the problems for these 12 million illegals that are here in our country," Boehner said.
By Deirdre Walsh
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