JAKARTA, Indonesia – A former general, Susilo Bambang Yudhoyono, took a seemingly unassailable lead yesterday in Indonesia’s presidential election, cheering investors amid hopes he will introduce much-needed economic reforms and provide firm leadership in the war on terror.

But in a sign of the challenges facing the next leader of the world’s largest Muslim nation, separatist rebels in the war-torn province of Aceh vowed that the bloody conflict would continue regardless of any change at the top.

The Jakarta stock market reacted to Mr. Yudhoyono’s apparent landslide by closing at an all-time high yesterday. Mr. Yudhoyono was expected to move quickly to announce Cabinet posts and set a new policy agenda to deal with problems facing the country, including rampant graft, aides said.

With over 80 million votes counted, or about two-thirds of the ballots cast in Monday’s election, Mr. Yudhoyono was leading with 61%, while the incumbent president, Megawati Sukarnoputri, had 39%, according to the General Election Commission.

The Washington-based National Democratic Institute said its “Quick Count” survey gave Mr. Yudhoyono 60% of the vote and 40% to Ms. Megawati. Monday’s poll passed off peacefully and foreign monitors pronounced it fair. The election was the first in which Indonesian voters chose their leader directly, and was a key step in the sprawling nation’s transition to democracy.

Mr. Yudhoyono has declined so far to claim victory and Ms. Megawati did not concede.