Tens of thousands of troops and policemen were deployed to safeguard the two-day vote, reflecting growing security concerns less than a month after a Russian airliner crashed in Egypt's Sinai Peninsula, killing all 224 people on board.
Russia has said the crash was caused by an onboard bomb, and a local Islamic State affiliate has claimed the Oct. 31 attack.
The new, 596-seat legislature is due to hold its inaugural session next month after a runoff is held in early December. Egyptians voted last month in 14 provinces, the vote's first phase, with a turnout of nearly 27 per cent.
That was the lowest turnout in any vote, except one for a toothless upper chamber in 2012, since the ouster of autocrat Hosni Mubarak in a 2011 popular uprising.
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El-Sissi was elected last year. Since Morsi's ouster, authorities have launched an all-out crackdown against the Muslim Brotherhood, his now-banned Islamist group, jailing thousands and killing hundreds in street clashes with security forces.
The young liberal and pro-democracy activists who spearheaded the 2011 uprising have also been swept up in the crackdown, with authorities detaining dozens of them, mostly for breaching a law adopted in November 2013 that effectively bans street demonstrations.