Election officials have begun counting votes in Egypt's divisive presidential run-off election.

It pits the Muslim Brotherhood's candidate against an ex-prime minister from the ousted regime.

Polls closed two hours later than scheduled after Egypt's electoral commission extended voting hours, in part to allow voters a chance to cast their ballots in the relative cool of the evening hours.

They are choosing between former air force chief Ahmed Shafiq, the last prime minister under ousted president Hosni Mubarak, and the Muslim Brotherhood's candidate, Mohammed Mursi.

At a press conference before the polls closed, election commission head Hatem Bagato told reporters that turnout appeared to be lower than the first round held on 23 and 24 May.

Official results are expected on 21 June, but initial numbers are expected to come in immediately, with possible indications of trends emerging by the early hours of tomorrow morning.

The election comes against a backdrop of legal and political chaos, with the Muslim Brotherhood set on a confrontation path with the ruling military after it yesterday ordered the Islamist-led parliament dissolved.

As the polls closed, at 9pm Irish time, state television said Egypt's ruling military council issued an amended constitutional declaration.

It is expected to hand them legislative and budgetary power after a court on Thursday annuled the elected parliament.