Sisi supporters won a landslide in the first leg and are expected to repeat their performance on Sunday and Monday when voting takes place in the capital Cairo and 12 other provinces.
Sisi cast his ballot at a girls` school in Cairo soon after voting opened at 9 a.m. (0700 GMT). State television once again showed footage of largely empty polling stations.
The government announced it was giving public sector workers half a day off on Monday to encourage them to cast their ballots.
Many who abstained said they felt the polls offered little genuine choice in the absence of the main opposition Muslim Brotherhood and other critics and that parliament would change little in lives dominated by the struggle to earn a living.
"There is no reason to vote, these elections don’t mean anything. All these candidates are running so they can get MP perks," said Hassan, a 21-year-old student who declined to give his full name.
Egypt`s top Muslim cleric Sheikh Ahmed al Tayeb, head of al-Azhar, the center of Islamic learning in the country, likened boycotting to disobeying one`s parents, a grave sin in Islam.
"I urge everyone, especially the youth, to participate and cast their ballots," Tayeb told journalists outside the polling station where he cast his vote.
"We tell boycotters to stop this immediately; Egypt is like your mother, boycotting is like disobeying your parents."
Egypt`s last parliament was elected in 2011-12, in the first election after the popular uprising that ended Hosni Mubarak`s 30-year rule. Voting then was marked by long queues and youthful excitement. The Muslim Brotherhood, long the country`s main opposition movement, won about half the seats.
A court dissolved that parliament in mid-2012. A year later, Sisi, then military chief, removed President Mohamed Mursi of the Brotherhood from power after mass protests against his rule.
Egypt`s oldest Islamist organization was banned, declared a terrorist organization and thousands of its members were jailed.
When it ousted Sisi, the army won the backing of other political groups by promising prompt parliamentary elections. Instead, Sisi went on to win a presidential vote in 2014. Parliament polls will finally be completed this month.
VOTER FATIGUE
The new parliament will contain 568 elected members -- 448 elected on an individual basis and 120 through winner-takes-all lists. Sisi may appoint up to a further 28 lawmakers.
On Sunday and Monday, candidates will be vying for 222 individual seats and 60 list seats.
"For the Love of Egypt", a loyalist electoral alliance led by former intelligence officer Sameh Seif Elyazal, won all 60 list-based seats contested in the first round, which covered Egypt`s second city of Alexandria, the province of Giza, which includes parts of Cairo west of the Nile, and 12 other provinces.
In the absence of the Brotherhood, critics say the ballot offers many names but little genuine choice.
A list of socialist and liberal parties which would have presented the main opposition choice eventually withdrew, leaving the field dominated by Sisi supporters, Mubarak-era figures, provincial notables and businessmen.
These figures performed well in round one.
The lack of interest in voting reflects disillusionment with politics but also voter fatigue after a turbulent few years.
Egyptians have participated in two presidential elections, two parliamentary elections and three constitutional referendums since the 2011 uprising. Polls often drag out over several weeks with different rounds and run-offs draining them of momentum.
"Zamalek is so empty because all the schools are closed; traffic is great. I wish we had elections here all the time," said Ahmed Abbasi, a 44-year-old electrician.
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