Egyptians were voting on Saturday in a run-off presidential election pitting an Islamist against Hosni Mubarak's last premier amid political chaos highlighted by uncertainty over the future role of the army.

Voters braved the heat to cast their ballots, as police and army troops deployed nationwide for the highly divisive election. Voting was extended by an hour to 1900 GMT.

Former air force chief Ahmed Shafiq, who served as ex-president Mubarak's prime minister in the last days of the Arab Spring-inspired uprising that toppled him, is vying for the top job against Muslim Brotherhood candidate Mohammed Mursi.

"I'm voting for Mursi because I don't want Shafiq to win. I'm scared of Mursi but I'm more scared of Shafiq," said Nagwan Gamal, 26, a teaching assistant.

The race has polarised the nation, dividing those who fear a return to the old regime under Shafiq from others who want to keep religion out of politics and fear the Brotherhood would stifle personal freedoms.

"I will vote for the one who will guarantee security and safety for our community," said Makram, a Coptic Christian voter, from a polling station in the Shoubra neighbourhood.

"I don't know how to feel," said Nancy Abdel Moneim, outside a polling station in Manial.

"I'm with the revolution so I voted for Mursi ... But frankly I'm scared of one and scared of the other, so I picked the one I'm least scared of."

The new president -- who will inherit a struggling economy, deteriorating security and the challenge of uniting a nation divided by the uprising -- will step into the role with no constitution and no parliament in place.

Mursi voted in his hometown of Zagazig in the Nile Delta province of Sharqiya, mobbed by a crowd to which he pledged that "the revolution will continue."

Shafiq, surrounded by supporters and security protection, voted in Cairo.

The election comes against the backdrop of a series of steps that have consolidated the ruling military's power, infuriating activists and boosting the boycott movement.

High-profile activists and celebrities have called on Egyptians to abstain or spoil their ballots, including film star and political activist Amr Waked, who said he was boycotting the vote for a variety of reasons.

"I reject the military-managed process, there is no clear authority for the president, and the fact that Shafiq is allowed to run," he said.

On Thursday, the Supreme Constitutional Court ruled certain articles in the law governing parliamentary elections to be invalid, thus annulling the Islamist-led house.

The Brotherhood won 47 percent of the body's seats in a drawn-out process between November last year and February.

The top court also ruled unconstitutional the "political isolation" law, which bars senior members of Mubarak's regime and top members of his now-dissolved party from running for public office for 10 years -- legislation that had threatened to disqualify Shafiq.

The rulings have put legislative power back in the military's hands and have guaranteed that Shafiq, perceived to be the army's candidate, stays in the race.

That, in addition to a recent justice ministry decision granting army personnel the right to arrest civilians, is proof of the army plans to anchor itself in power, activists say.

They accuse the Supreme Council of the Armed Forces (SCAF), which took power when Mubarak was ousted, of staging a "counter-revolution."

"This series of measures shows that the SCAF, the head of the counter-revolution, is adamant to bring back the old regime and the presidential elections are merely a show," six parties and movements said in a statement.

Hesham Sallam, a researcher at Georgetown University, said the latest steps are consistent with the military's management of the transition from Mubarak's rule.

"It is clear that SCAF has been pushing its vision, which is of a deep state protected and sealed from representative and elected institutions," Sallam said.

The official results of the presidential election are expected on June 21.

"Irrespective of who wins, you don't know who will be president but you know what kind of presidency it will be. One that is subservient to SCAF. Whether that will hold is another question," Sallam said.