AdvancED has threatened to strip the district of its accreditation if the board blocks the investigation.
Colleges use the accreditation to determine if applicants come from quality schools, and losing it could make it harder for students to get into the university of their choice or student loans.
AdvancED announced it intended to investigate last year after it got a complaint from the NAACP.
The NAACP has been a vocal opponent of the board's recent decision to do away with school assignments based on diversity in favor of sending students to schools closer to their homes.
AdvancEd says it intends to review actions and decisions -- like how new policies have been made, what's been done in the move toward community schools, and how the seat voucher system works for public meetings -- made by the Wake County School Board since January 1, 2010.
Some members of the Wake School Board who support the neighborhood schools concept have questioned the motivation of the investigation.
Still, the board voted 6-2 Tuesday to cooperate with AdvancED. Board members Chris Malone and Deborah Prickett voted against.
Malone said in comments during a meeting Tuesday that AdvancED has accredited low performing schools and stripped others of accreditation unfairly. He said he would rather seek accreditation from a different organization.
"I think they can be fair. It remains to be seen whether they will be or not. I certainly have all hope that they will and to that end, I will be and I will give them what they need," he said.
School board member Keith Sutton - who's on the minority that opposed changing the school assignment policy - was more positive.
"We've received countless emails encouraging us to keep the accreditation intact. I would think the community speaking up, probably was the tipping point," he offered.