A school board member, Interim Superintendent Donna Hargens, the attorney representing Wake schools, and other staffers met for about two hours with the Department of Education officials.
The meeting came after National NAACP president Ben Jealous announced his group had filed the complaint in September.
Jealous and North Carolina NAACP President William Barber said Wake's new policies violate the law which says that the recipients of federal funds cannot discriminate on basis of race, color, or national origin.
The U.S. Department of Education spends more than $77 million a year in Wake County.
The current majority on the Wake County School Board voted to move away from its long-standing diversity policy, and toward a community-based school assignment plan in a series of contentious meetings earlier this year.
Board members who supported the new policy - and spoke with ABC11 after the September announcement - said the old policy did not work.
"The past plan that did have diversity included tended to be a good public relations act, but it failed terribly when it came to academics," said Wake County School Board Chairman Ron Margiotta.
School board member Keith Sutton - who attended Tuesday's meeting - said he and other board members were not invited, but wanted to attend given what's at stake.
"I think the biggest potential of course, would be loss of funding," he told ABC11.
But school board attorney Ann Majestic told ABC11 after the meeting that the board has not broken the law.
But, Sutton said he feels federal investigators will find that some decisions the board majority has made are questionable.
"I think that is certainly their concern, and I think some of the decisions that we've made have the potential of having an adverse impact on particularly African-American students and students of poverty," he offered.
Margiotta was unable to attend Tuesday's meeting because of a family emergency.