The Muslim Brotherhood's Mohammed Morsi has officially won Egypt's presidential election and will be the country's next president, the electoral commission has announced.

Morsi picked up 13.2 million votes out of just over 26 million, giving him about 51 per cent of the vote. His competitor, Ahmed Shafiq, the final prime minister under Hosni Mubarak, received 12.3 million. More than 800,000 ballots were invalidated.

Farouq Sultan, the head of the election commission, delivered a long speech before announcing the results in which he defended the body's "independence and integrity" amidst what he called meddling by unnamed political factions.

The two candidates filed 456 complaints about the electoral process, Sultan said, most of them allegations of either forgery or Christian voters being blocked from polling stations in Upper Egypt. The vast majority of those complaints were dismissed.