McCain, asked Sunday on ABC's "This Week" about Babeu, said he thought of him as a friend.
"I do not know the details, except what has been published in the media," he said. "And I'm sure there will be a thorough and complete investigation, if there is any allegation of wrongdoing. All I can say is that he also deserves the benefit, as every citizen does, of innocence until proven guilty. But I appreciate the support that he gave me in my campaign and always will."
Arpaio, a longtime ally, distanced himself.
"All I can say is he's the sheriff of Pinal County, and it's up to him to face his issues, not me," Arpaio told The Arizona Republic. He said Babeu has been "begging" for an endorsement in the congressional primary.
"I don't even think I'm going to get involved," Arpaio said. "We'll see what happens with Babeu."
Just last weekend, Babeu gave a speech at the Conservative Political Action Conference in Washington, D.C., reiterating his criticism of Obama, the Justice Department's failed "Operation Fast and Furious" gunrunning investigation and seeking support for his congressional campaign.
Babeu has been something of an enigma since he appeared on the scene. He was elected to the city council of his hometown of North Adams, Mass., at age 18, and came to Arizona shortly after losing an election for North Adams mayor in 2001.
He became a Chandler police officer and in November 2008 defeated a Democratic incumbent to become sheriff.
Along the way, he served in the Army National Guard as both an enlisted man and an officer, retiring from the Arizona Guard as a major after serving stints in Iraq and along the U.S.-Mexico border.
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