TAHLEQUAH, Okla. — The challenger in the embattled election to lead one of the nation's largest American Indian tribes was ahead after an initial vote count Sunday, but it was too early to declare a winner in a race that has been marred by months of complications.

The Cherokee Nation Election Commission counted votes that were cast in person since the new election began Sept. 24. The unofficial tally showed Cherokee Nation councilman Bill John Baker with 61 percent of the vote, receiving 6,223 votes compared to 4,046 for former Principal Chief Chad Smith.

But as many as 12,000 absentee ballots still have to be counted. The winner may not be known until Wednesday.

The election was ordered by the tribe's Supreme Court after the results of a June 25 election were invalidated. Smith and Baker were each twice declared the winner in recounts, and questions were raised about how the ballots were handled and stored. Smith was chief until a temporary replacement was named after the June election.

Also complicating the election were lawsuits filed by the descendants of slaves owned by Cherokees, known as freedmen, who won an agreement making them eligible to vote as they fight efforts by the Cherokee administration to cut them out of the tribe.

Smith has campaigned for the last decade to remove non-Cherokee freedmen from the tribe's voter rolls. Baker also backed their removal but not as vocally, and he is believed to have the support of many freedmen.

Voting stretched from Sept. 24 until Saturday to accommodate hundreds of freedmen who were expected to cast ballots. The ballot counting was watched by members of both campaigns, along with election monitors from the Carter Center in Atlanta.

Smith is seeking a fourth four-year term as leader of Oklahoma's largest American Indian tribe and one of the most powerful and influential tribes in the country.

Baker, a Tahlequah furniture store owner and longtime Cherokee Nation council member, has criticized Smith on numerous fronts, including accusing Smith of not using enough revenue from tribe-operated casinos to fund health clinics and care for the elderly.

Baker and Smith each expressed confidence Sunday that the absentee votes would secure the election in his favor.

"We are cautiously optimistic," said Baker's spokeswoman, Linda Gray Murphy.

Smith, in an emailed statement, said: "With still about half the votes left to count, I'm still very confident with how this will turn out."

The freedmen agreement that allowed them to vote was a temporary reprieve in the long-running debate over whether they should be given full Cherokee Nation membership rights. The lawsuit brought by the freedmen, who are seeking to keep their right to vote and other tribal benefits after tribe members voted to cut them off, is continuing in federal court.