Indonesian candidate Prabowo Subianto walks with his team after a meeting in Jakarta on Sunday. Agence France-Presse/Getty Images

JAKARTA, Indonesia—Indonesian presidential contender Prabowo Subianto filed a complaint against an elections agency on Monday, a step in what's expected to be a broader legal challenge to the July 9 election.

The complaint concerns more than 200,000 ballots cast in Jakarta and would have no direct bearing on the contest that the capital's governor, Joko Widodo, appears to have won by millions of votes, according to unofficial results. The complaint was filed to an ethics council and can't lead to a revote—only to the possible dismissal of elections officials.

The challenge, though, was widely seen as a sign that the Subianto camp is digging in for a wider battle over the official results of the poll, which are expected to be announced Tuesday. The electoral contest has been hard fought between two men with starkly different personalities vying to run the world's third largest democracy.

Mr. Subianto, a former military man and one-time son-in-law of the late authoritarian ruler Suharto, who was ousted in 1998, has appealed to voters longing for strong leadership. Mr. Widodo, a former mayor of a midsize city, has cast himself as an ordinary man of the people with a knack for getting things done.

One of the men will replace President Susilo Bambang Yudhoyono, who steps down after reaching a 10-year term limit in October. The national elections commission has nearly completed certifying vote tabulations. As of Monday, it had completed counting in 22 of 33 provinces, with Mr. Widodo leading with 51.4% of the votes.

Mr. Subianto's team has said it would appeal to the country's Constitutional Court after the official announcement of results Tuesday.

"Judging from what they did today, that appears likely," said Saldi Isra, a law professor at Andalas University in West Sumatra. "But most likely the court will dismiss whatever case they bring," given that the bar is high for presenting elections cases at the Constitutional Court.

A major electoral legal challenge could leave Indonesia in a state of political limbo, prolonging tensions in the wake of an election in which more than 130 million voters cast ballots. Indonesia has no history of widespread election violence, but the divisive nature of the election and its outcome has raised fears of isolated incidents of unrest.

Mr. Subianto's team filed its complaint Monday against Jakarta's regional elections commission to an ethics council, saying the poll body failed to address voting irregularities at thousands of polling stations in the capital during the vote.

The elections agency "didn't do anything about [ineligible voters] flooding in to polling stations," said Mohammad Taufik, head of Mr. Subianto's Jakarta campaign team. "We have to take action against them."

Staff at the ethics council said they would quickly assess whether there appeared to be a violation. The national elections agency meanwhile said that its national and regional offices, including the one in Jakarta, had fulfilled their responsibilities concerning reports of irregularities in the vote.

Mohammad Taufik, head of the Jakarta campaign team of Indonesian presidential contender Prabowo Subianto, shows a government receipt of complaints he lodged with an elections ethics council in Jakarta. Ben Otto

In past elections, legal challenges have had no effect on the final outcome. During legislative elections in April, only 21 of about 900 court challenges resulted in action; all others were dismissed.

In this election, Indonesia's third direct presidential poll since the ouster of Mr. Suharto, the level of oversight was unprecedented, with tens of thousands of volunteers, campaign workers, and media overseeing the vote and counting process.

The commission said it plans to finish the vote-counting process Tuesday, then invite both Mr. Widodo and Mr. Subianto to its offices to accept the results.

—Anita Rachman
and I Made Sentana
contributed to this article.

Write to Ben Otto at