AFGHANS headed to the polls to vote for a new president on Saturday amid high security after the Taliban vowed to disrupt the elections, warning citizens to stay home or risk being hurt.

Already, at least 15 people have been injured in the southern city of Kandahar after a bomb blast at a local mosque where a polling station is located.

The leading contenders for the presidency are the incumbent Ashraf Ghani and his partner in the five-year-old unity government, Abdullah Abdullah, who has alleged abuses of power by his opponent.

Fear and frustration at the relentless corruption that has characterised successive governments rank high among Afghan concerns.

Tens of thousands of police, intelligence officials and Afghan National Army personnel have been deployed throughout the country to protect nearly 5,000 election centres.

The Taliban said it will take particular aim at Afghanistan's cities.

Fear and frustration at the relentless corruption that has characterised successive governments ranks high among the concerns of Afghanistan's 9.6 million eligible voters.

The country has also been rattled by an upsurge in violence in the run-up to the elections, following the collapse of US-Taliban talks to end America's longest war.

One of the first reports of violence came from southern Afghanistan, the former spiritual heartland of the Taliban. A bomb attack on a local mosque where a polling station was located wounded 15 people, a doctor at the main hospital in Kandahar said.

The wounded included a police officer and several election officials, along with voters. Three are in a critical condition.

An official in Afghanistan's north later said insurgents are firing mortars on the city of Kunduz.

Ghulam Rabani Rabani, a council member for Kunduz province, said the Taliban is also attacking Afghan security forces in two locations outside the city in running gun battles.

Even in the early hours of voting, complaints had begun to be raised such as polling stations in the capital's Wazir Akbar region opening late, and biometric machines which were aimed at curbing fraud not working.

In the northern Taimani area of mostly ethnic Hazaras, two thirds of the voting registration papers had yet to arrive and angry voters were told their names were not on the list.

Abdul Ghafoor, who spoke on behalf of dozens of men waiting to cast their ballot, said that of about 3,000 registered voters only 400 appeared on the list that had arrived at the centre.

Mr Ghafoor said he was told to return at 2pm and that he would be allowed to vote even if his name was not on the list and without using the biometric machine.

"But how can they do this? My vote won't count if I am not on a list," he said.

Afghanistan's chief election official later said polls will stay open for an extra hour until 5pm local time.

Hawa Alim Nuristani, head of the Independent Election Commission, said officials wanted people still waiting in line a chance to cast their vote.

Tens of thousands of police, intelligence officials and Afghan National Army personnel have been deployed throughout the country to protect the 4,942 election centres.

Authorities said 431 polling centres will stay closed because it was impossible to guarantee their security since they were either in areas under Taliban control or where insurgents could threaten nearby villages.

In Kabul, traffic was light, with police and the army scattered throughout the city, stopping cars and looking for anything out of the ordinary.

Outfitted in bullet-proof vests, their rifles by their side, soldiers slowed traffic to a crawl as they searched vehicles.

Larger vehicles were not being allowed into the capital on Saturday, which is normally a regular working day, but has been declared a holiday due to the elections.

Neighbouring Pakistan, which is routinely accused of aiding the insurgents, announced it is closing its borders with Afghanistan on Saturday and Sunday to boost security in the war-weary country.

Campaigning for Saturday's elections was subdued, only going into high gear barely two weeks ahead of the polls as most of the 18 presidential candidates expected a deal between the United States and the Taliban to delay the vote.

But on September 7, US president Donald Trump declared a deal that seemed imminent dead after violent attacks in Kabul killed 12 people, including two US-led coalition soldiers, one of whom was American.

While many of the presidential candidates withdrew from the election, none formally did so, leaving all 18 candidates on the ballot.

Elections in Afghanistan are notoriously flawed and in the last presidential polls in 2014, allegations of corruption were so widespread that the United States intervened to prevent violence.

No winner was declared and the US put together the unity government in which Mr Ghani and Mr Abdullah shared equal power - with Mr Ghani as president and Mr Abdullah as chief executive, a newly created position.

Constant bickering and infighting within the government frustrated attempts to bring in substantive legislation as security, which has been tenuous, continued to deteriorate, frustrating Afghans and causing many to flee as refugees.