Obama announced the changes on Friday and said he wants the NSA to get approval from the courts before searching a database.
The government will also only pursue calls that are two steps away from a suspected number, instead of three.
Although Hayden, a retired Air Force general, says he supports much of Obama's plan, he questioned some of the changes during his appearance on "Fox News Sunday."
"Now, look, if the third hop weren't useful from time to time, we wouldn't have been doing it in the first place," he said. I'm a little more concerned about going to the court every time you want to clear the data ... that's a professional intelligence judgment. I don't know what role the court has in adding value."
Sen. Patrick Leahy, who was also on the show Sunday, spoke in favor of the measures, but said the Senate will still consider legislation on the matter.
"There's a concern that we have gone too much into Americans' privacy," he said. "There's still going to be legislation on this."