Nine years ago, law professor Lloyd Cohen filed a federal civil rights complaint alleging racial discrimination in admissions to Fairfax County’s prestigious Thomas Jefferson High School for Science and Technology.

But he didn’t argue that the system was biased against black and Latino students, as the Fairfax chapter of the NAACP and a local advocacy group alleged in a similar complaint filed Monday with the Department of Education. African American and Latino students make up 4 percent of the rising freshmen at Thomas Jefferson, or TJ, but make up 32 percent of the county’s entire student body.

Instead, Cohen contended that it was white students who were losing out, the deck stacked against them as the school system sought to boost black enrollment at the high-flying school.

Fairfax officials reject that accusation. The school system “was not discriminating against whites in the admissions process,” spokesman John Torre wrote in an e-mail.

Federal authorities ruled on Cohen’s complaint in a letter dated May 25. Apologizing for the “substantial delay” in responding, they said that school systems may legally consider race in admissions decisions — but in the case of TJ, they “did not find sufficient evidence that race was a factor in admissions” between 2000 and 2004, the period in question.

Cohen, a father of three Fairfax graduates — including two TJ alumni — filed an appeal in early June. So, now, federal authorities are faced with two civil rights complaints — each based on a different perspective on who is losing out in the battle to attend TJ and each a sign that the vaunted Fairfax school occupies a special role as a lightning rod for arguments about race, equity and opportunity.

“The community believes in the value of Thomas Jefferson,” said Ilryong Moon (At Large), chairman of the county School Board. “That is why a lot of people are taking an interest, rightfully so.”

Cohen’s complaint was distilled from a long article he wrote in 2003 for the Albany Law Review, in which he used statistical tools and other information to analyze TJ admissions decisions made in 2002.

That year, 11 black students made it into a pool of about 800 semifinalists based on the strength of their grades and scores on a math admissions test. Ten of them — including some who scored lower than white students who were rejected — were admitted after teacher recommendations and essays were considered.

According to Cohen’s analysis, black students were substantially more likely to be admitted than white students with similar credentials. Hispanic and Asian students also had an advantage over their white counterparts, he wrote, although a smaller one.

“The true purpose of the current admissions regime is to engage in invidious racial discrimination,” Cohen wrote.

His argument triggered a response from then-Superintendent Daniel Domenech, who called Cohen’s accusations “offensive and untrue,” and it touched off a firestorm at TJ and across Fairfax.

Cohen said he was working from a basic set of principles to which he still adheres.