Tunisians voted Sunday in the runoff of the country's first free presidential election, with authorities urging a big turnout to answer efforts to disrupt the final leg of a four-year transition.

Just hours before polls opened at 8:00 am (0700 GMT), troops guarding ballot papers in the central region of Kairouan came under attack and shot dead one assailant and captured three, the defence ministry said.

Prime Minister Mehdi Jomaa condemned what he said was a "desperate attempt" to disrupt the embrace of democracy in the country that triggered the Arab Spring.

"The best response is to turn out calmly and in numbers," Jomaa told Mosaique FM radio.

The second round vote pits 88-year-old favourite Beji Caid Essebsi, leader of the anti-Islamist Nidaa Tounes party, against incumbent Moncef Marzouki, who held the post through an alliance with the moderate Islamist movement Ennahda.

Authorities deployed tens of thousands of soldiers and police to provide polling day security.

Ahead of the vote, which sets Tunisia apart from the turmoil of other Arab Spring countries, jihadists had issued a videotaped threat against the North African state's political establishment.

It is the first time that Tunisians have freely elected their president since independence from France in 1956.

After three hours of voting, turnout reached 14.04 percent, election organisers said. Polls were due to close at 6:00 pm (1700 GMT) and the result could be announced as early as Monday evening.

A first round held on November 23 saw Essebsi win 39 percent of the vote, six percentage points ahead of Marzouki, a 69-year-old former rights activist installed by parliament two months after December 2011 polls.

The vote is the country's third in as many months, after Nidaa Tounes won an October parliamentary election, making Essebsi favourite to be the next president, but with powers curbed under constitutional amendments to guard against a return to dictatorship.

The campaign was marked by mudslinging, with Essebsi refusing to take part in a debate with Marzouki, claiming his opponent is an "extremist".

Essebsi insists that Marzouki represents the Islamists, charging that they had "ruined" the country since the 2011 revolution which toppled veteran ruler Zine El Abidine Ben Ali and gave birth to the Arab Spring.

Marzouki in turn accused Essebsi, who served as a senior official in previous Tunisian regimes, of wanting to restore the old guard deposed in the revolution.

But after casting his vote, Marzouki vowed to respect the verdict of the ballot box.

"The rules of the democratic game require that each of us accepts the outcome of the vote in a sporting spirit," he said.

Voters said they regretted the lack of restraint shown by candidates during the campaign but believed the country was on the path towards democracy.

"Our candidates and their policies perhaps aren't the best but we're moving forward -- the dictatorship is over," said Tunis shopkeeper Mohammed Taieb.

In an Internet video posted Wednesday, jihadists claimed the 2013 murder of two secular politicians that plunged Tunisia into crisis, and warned of more killings of politicians and security forces.

Last year's murders had threatened to derail Tunisia's post-Arab Spring transition until a compromise government was formed in January this year.

In the video, jihadist Abou Mossaab called on Tunisians to boycott the poll runoff, saying the authorities "are turning you into infidels with these elections".

But defence ministry spokesman Belhassan Oueslati said he did not believe the jihadists were behind Sunday's pre-dawn attack.

"The vigilance of the soldiers and the swiftness of their response thwarted this operation and led to the death of a man armed with a hunting rifle and the arrest of three suspects," Oueslati told AFP.

"Generally, the terrorists don't use hunting rifles," he added.

In addition to the jihadist threat, Tunisia faces major challenges.

Its economy is struggling to recover from the upheaval of the revolution, and there are also fears of widespread joblessness causing social unrest.

The International Crisis Group think tank has said Tunisia was the "last hope" for a peaceful transition to democracy, setting it apart from other Arab Spring countries such as Libya and Egypt.

"In the context of the meagre harvest of the Arab Spring, Tunisia remains the last hope for a successful democratic transition," it said.