The flights in question are the same flights her campaign committee failed to report landing a $30,000 fine from the State Board of Elections.
"We've initiated an investigation based on some information from the State Board of Elections," Wake DA Colon Willoughby said.
Willoughby requested the SBI probe several weeks ago. He says his queries didn't involve the governor, but wouldn't say who the FBI subpoenaed.
"I can only speak to what our office is doing with the assistance of the SBI," he said.
The governor and her staff have said for the past year that an internal review found the unreported flights and that the campaign voluntarily reported the potential problems to the elections board.
But the board found that the campaign had information on 37 flights in mid-2007, but only reported 18 of them before Election Day of the following year. Perdue's committee attorney couldn't explain why the campaign information was withheld.Perdue has said she never intended to hide any aspects of her campaign.
But that didn't allay doubts for state Republican Party Chair Tom Fetzer.
"We have believed all along it would take a criminal investigation to get to the truth," he said. "We still stand by our assertion that Governor Perdue and her campaign broke laws and attempted to cover-up actions with lies."
Meanwhile, the North Carolina Democratic Party called news of the federal investigation partisan politics.
"Eleven days before a crucial election affecting the direction of our nation and state, we have learned that the Republican U.S. Attorney has apparently chosen to serve subpoenas and open yet another investigation into a Democratic elected official. The timing of these events would lead any reasonable person to have serious questions about this new investigation. The North Carolina Democratic Party will continue to focus on the matter at hand - working to elect Democrats across the state who will continue moving North Carolina forward," offered Andrew Whalen, Executive Director of the North Carolina Democratic Party in a statement.
"It is a sad commentary when federal agents and federal prosecutors have to come in," said Frank Perry with the Foundation for Ethics and Public Service. "Grand juries have a mind of their own and they operate according to strict federal secrecy rules."
Perry is the former head of Raleigh's FBI office. He says fears about timing and state and federal agencies butting heads are unfounded.
"I don't think that will happen," Perry said. "We have some smart attorneys at the state level as well as the federal level and they'll work that out."
Perdue said earlier this month that she's confident the state investigation won't turn up intentional criminal wrongdoing.
"Since this is a federal investigation, it would be inappropriate for me to make any additional comments or answer any questions about it," Perdue went on to say in her statement. "North Carolina, a state we all love, as we all know, is in a critical time in its existence. I will continue to use all my time and energy to address and resolve the challenging issues facing our state."
Perdue is just the latest high profile North Carolina Democrat to be the target of an investigation. Former Governor Mike Easley is also under investigation by a state prosecutor for flights he took while campaigning. The outcome of that investigation is expected later this year.
Former presidential candidate John Edwards is the subject of a federal probe by investigators who want to know if he used campaign funds to carry out his affair with Rielle Hunter.
Both Easley and Edwards have denied any wrongdoing.