The Justice Department's harsh condemnation of the law is "an insult," McCrory told CNN's Jake Tapper on "The Lead," adding, "it's a political statement instead of a legal statement."
Signed into law in March, House Bill 2 prohibits people from entering bathrooms that do not match the sex on their birth certificates -- a distinction that opponents, now including top federal law enforcement officials, have called a violation of the Civil Rights Act.
On Monday, the Justice Department and North Carolina filed dueling lawsuits, setting the stage for a long legal battle that could be destined for the Supreme Court.
Attorney General Loretta Lynch called the legislation "state-sponsored discrimination against transgender individuals who simply seek to engage in the most private of functions in a place of safety and security."
"It was not so very long ago that states, including North Carolina, had other signs above restrooms, water fountains, and on public accommodations, keeping people out based on a distinction without a difference," the North Carolina native said at a news conference announcing the suit.
McCrory, a Republican running for reelection this year, rejected Lynch's comments and described any comparison to the Civil Rights era of the 1950s and 1960s as "totally irresponsible."
He also defended the public rationale for the law and argued that the presence of transgender children in the facilities they prefer could infringe on their peers' privacy rights.
"There's an expectation of privacy for the other girls or other boys in their junior high locker rooms or shower facilities, that the only other people coming into there are people of the same gender, or built as the same gender," he said. "We need to work through these problems and not throw hand grenades at this issue because it's a new, sensitive issue on all sides."
Still, McCrory said he had no intention of pursuing a "bathroom bill" until the city council in Charlotte passed a wide-ranging anti-discrimination bill that included protected bathroom access for transgender people.
"I had no interest in this subject," he told Tapper, again blaming Democrats in the city where he served a record 14 years as mayor between 1995 and 2009.
Since he signed the bill over former colleagues' objections, North Carolina has emerged as a national political battleground
, with businesses withdrawing plans to expand into the state and entertainers like Bruce Springsteen, Demi Lovato, Nick Jonas, Pearl Jam and Boston canceling scheduled performances.