"I thought it was allowed. I knew past secretaries of state used personal email," she told CNN's Wolf Blitzer on "The Situation Room, saying the rules were only recently improved.
"They were not a model of clarity and it seems like there is still more work to do on that," she said.
Clinton reaffirmed that she had made an error in using a private email server, saying, "It was still a mistake. If I could go back, I'd do it differently."
She also attacked Donald Trump, who on Thursday clinched the necessary delegates for the Republican presidential nomination. She pushed back on his accusation that she wanted to "abolish" the Second Amendment as "absolutely ridiculous" and called it another example of his "fantasy campaign."
"This man, who is an unqualified loose cannon, is within reach of the most important job in the world. So it should concern every American," Clinton said. "I know that Trump thinks this is a point of pride, that people like me or President (Barack) Obama raise questions and criticize him. But it's not. This is not a reality show. It's not just politics. It's really serious."
Clinton's campaign was rocked this week by a State Department Inspector General reportreleased Wednesday that found she failed to follow the rules or inform key department staff regarding her use of a private email server.
The report, which was provided to lawmakers, said, "At a minimum, Secretary Clinton should have surrendered all emails dealing with Department business before leaving government service and, because she did not do so, she did not comply with the Department's policies that were implemented in accordance with the Federal Records Act."
In producing the report, the Inspector General's office interviewed former Secretaries of State Madeleine Albright, Colin Powell and Condoleezza Rice.
Clinton and several of her staff members during her tenure declined to be interviewed, the report said.
"Everything I had to say was out there," she told Blitzer.
Clinton on Thursday also reacted to a possible debate between Trump and her lingering Democratic rival, Bernie Sanders, which the candidates are now entertaining.
"I don't think it's serious," she said. "It's not going to happen."