Robert N. Barnette Jr., who has led the Virginia State Conference NAACP since August when the previous presi- dent was removed, will hold the top post in the civil rights organization for the next two years after emerging victorious in a controversial election.

Mr. Barnette, 67, a retired safety engineer and president of the Hanover County Branch NAACP for seven years, was installed Sunday as state NAACP president after winning a three-way race.

He received 43 percent of the votes that 119 qualified delegates cast at the 84th state convention held last weekend at a Henrico County hotel.

Mr. Barnette fended off challenges from Pastor Michelle Thomas, president of the Loudoun County Branch NAACP, who won 33 percent of the vote, and Carmen Taylor of Hampton, a past state NAACP president, who got 24 percent.

Two other candidates for president were disqualified at the last minute — along with 48 convention delegates who sought to cast ballots — under rules that had not been announced in advance and that conference veterans said had never applied before.

Also disqualified was a reform-minded candidate, Phillip Thompson, past president of the Loudoun County Branch NAACP and a state Executive Committee member, who was unopposed for state vice president, the No. 2 leadership post.

“They made up the rules to get the results they wanted,” said Mr. Thompson, who did not attend the conference but had agreed to allow Ms. Thomas to nominate him, a practice previously allowed.

In a statement, the state conference ignored the controversy. Instead, the conference highlighted the passage of new bylaws and approval of a new leadership structure, agreement to employ a research-based approach to civic engagement and assurances of a closer alignment with the national office staff and NAACP branches across the country.

Still, the way the election was carried out left Mr. Thompson and others rethinking their participation in a state organization that has struggled to maintain its membership numbers.

Total state NAACP membership is projected between 16,000 and 20,000 dues-paying members, or half the peak of the 1990s when more than 40,000 Virginians belonged, according to organization records.

The number of active chapters also has declined from more than 90 to around 60 that are up-to-date in payment of their annual assessments.

Mr. Barnette, saying he was “humbled and honored” to be elected, said his top priorities would include efforts to strengthen the organi- zation internally and to hire a new executive director to end national supervision.

He said during his tenure, the NAACP would continue to push for increasing the state minimum wage to $15 an hour and to raise the threshold for a felony charge of grand larceny from $500 to $1,500 as part of its policy agenda on social justice.

Mr. Barnette has been vested with more influence over the state’s governing Executive Committee than past presidents. The newly passed bylaws allow Mr. Barnette to appoint up to 28 committee chairpersons, who will join the seven regional vice presidents, six at-large members and the secretary and treasurer on the enlarged committee.

Even as he looked ahead, Mr. Barnette sought to sidestep concerns raised about the legitimacy of the election results. He said that the state turned the election over to two representatives of the national NAACP, Gloria Jean Sweet-Love of Tennessee, a national board member who in April was appointed to administer the Virginia State Conference, and Jonathan McKinney, a regional director who oversees NAACP operations in several states, including Virginia.

“The Virginia State Conference left it to them,” Mr. Barnette said, although he acknowledged that the disqualifications would not have happened if state rules were followed.

Ms. Sweet-Love and Mr. McKinney, who did not respond to Free Press requests for comment, cut the number of voting delegates by disqualifying people they said had paid local and state dues, but not national dues — a rule that conference veterans said had never been used before.

Ms. Sweet-Love also refused to allow the six delegates from Chesterfield County to participate in the election or to let their candidate, Tavorise Marks, to run for president.

The branch apparently failed to submit registration payments for the delegation ahead of the convention. Recognizing the problem was not of the delegation’s making, state officers, including Mr. Barnette, allowed the delegation to attend and participate in earlier votes on changing the organization’s bylaws.

However, Ms. Sweet-Love barred the delegation for not being properly registered. She also eliminated Shirley Ginwright, a past president of the Fairfax Branch NAACP, as a presidential candidate because she was not an elected delegate, which Ms. Sweet-Love said is a requirement. Mr. Barnette said the state bylaws do not impose such a requirement.

Ms. Sweet-Love also eliminated Mr. Thompson from the vice presidential ballot because he did not personally sign the candidate form, even though both he and others said that was not a state bylaw requirement. In the past, supporters could nominate without such a condition being imposed.

The upshot was that delegates who apparently were part of a reform coalition seeking to elect Ms. Thomas had their numbers sharply reduced. Protests over the rules proved unsuccessful.

And Ms. Sweet-Love, while running the election, also sought to steer votes to her favored candidates by speaking out on their behalf, while those running appeared before the delegates to make their pitch, according to people in the room. “Nothing like that has ever occurred,” one member said.

Separately, on Nov. 1, Ms. Sweet-Love engineered a reorganization of the state organization that critics see as reducing the influence of the large, urban chapters in Northern Virginia and the Richmond area. Under the approved plan, the urban chapters will be outnumbered by smaller, rural branches in seven large regions, a number reduced from 14.

The election took place at an NAACP gathering that already had come under fire for naming Dominion Energy as the title corporate sponsor after the company doubled its donation to $50,000.

Critics bashed the state NAACP for showing favor to the energy company even as the organization continues battling in federal court the company’s Atlantic Coast Pipeline plan to install potentially air-polluting equipment in a small, African-American farming community founded by former enslaved people in Buckingham County.

On Sunday as the convention closed, the state NAACP quietly killed a proposed but unsigned resolution to ban such donations because there was no evidence a branch had advanced it.