SARAJEVO - Nationalist candidates appeared headed for victory Monday in Bosnia’s three-way presidency, threatening new political instability in a country that still bears the scars of inter-ethnic war. Partial results showed the head of the Muslim SDA party, Bakir Izetbegovic, was set to win his second term as the Muslim member of the joint presidency, which also includes a Serb and a Croat representative.

The unwieldy arrangement is part of a political system created by the US-brokered Dayton peace accord that ended a 1992-95 ethnic war in which some 100,000 people were killed.

But although Bosnia-Herzegovina has been at peace since that bloodletting, Sunday’s general election, which also included parliamentary polls, laid bare mass discontent over the economy and division along ethnic lines.

With about 77 percent of ballots counted, Izetbegovic - the son of Bosnia’s late wartime leader Alija Izetbegovic - had 33.16 percent of the votes.

Izetbegovic, 58, all but claimed victory, saying that the nationalist SDA would emerge as the main power and the “basis for all future coalitions.”

Zeljka Cvijanovic and Dragan Covic were leading the race for the Serb and Croat members of the presidency respectively, both of them also from nationalist parties.

In addition to the three-man presidency, voters were choosing a Bosnian federal parliament.

Under the complex Bosnian system, voters also chose members of the assemblies that oversee the country’s two semi-autonomous halves - one the ethnic-Serb Republika Srpska and the other the Muslim-Croat Federation.

Finally, Serbs in their semi-autonomous region were also choosing a local president.

About 3.3 million Bosnians were eligible to vote on Sunday, but turnout was 54 percent, about two percent lower than in 2010 polls, reflecting widespread disenchantment with what is seen as the country’s corrupt and inefficient political class.

Unemployment is at 44 percent and in February mass protests broke out against the government’s failure to fight graft and enact the reforms required for Bosnia to enter the European Union.

Worryingly for a country struggling to put aside the trauma of its civil war two decades ago, the election also appeared to reinforce society’s splits along ethnic loyalties.

“No one can celebrate in this country. Those who won the largest number of votes will be put to the test,” the Sarajevo-based Dnevni Avaz daily commented.

“If those parties don’t take in the seriousness of the situation and the message sent by the population during February’s protests, what will come next will be much more violent,” the newspaper warned.

Election pitches were infused with nationalist rhetoric, particularly in attempts to woo ethnic Serb voters.

Their nationalist leader, Milorad Dodik, running for a new term as Republika Srpska’s local president, renewed threats that his entity might secede from the federal Bosnia - in other words renewing the kinds of aspirations that plunged Bosnians into a disastrous war in the 1990s.

“The aim of my policy is that we are less and less an entity and more a state,” Dodik told an election rally.

Ivana Saric, a student from Sarajevo, said she had voted for a small, multi-ethnic party, but she doubted many others would do the same.

“People are afraid to vote for major change, possibly because they are traumatised by the past. Twenty years ago they chose democracy. That brought them independence and then, later, war.”

Bosnia’s economic doldrums form a grim backdrop to the vote. Average monthly salaries are 415 euros ($525) and corruption that has plagued the country since its inception now costs taxpayers some 750 million euros annually, according to non-governmental organisations.

Major floods in May, which caused an estimated two billion euros in damages - roughly 15 percent of Bosnia’s gross domestic product - have further aggravated the economic situation.

And Bosnia’s EU aspirations have been put on hold by political deadlock since 2006 due to ethnic tensions.

Politicians from the three major ethnic groups have failed to agree on reforms needed for membership in the 28-nation European bloc, leaving Bosnia lagging behind its fellow Balkan countries.

Ahead of the vote, the European Union said in a statement that Bosnians needed to pressure elected officials into bringing “much-needed reconciliation” and to “close the gap with rest of the region and ensure progress towards the EU”.