First vote of post-Morsi era shows strength of support for direction country has taken since overthrow of president in July

Over 98% of participants in the first Egyptian vote of the post-Morsi era voted in favour of approving a new constitution, the country's electoral commission officially announced on Saturday.

Egypt's government hailed the result as a resounding show of support for the direction the country has taken since the overthrow of Mohamed Morsi last July.

"This is a wonderful day for Egypt, Egyptians and for democracy, despite the extraordinary circumstances," a spokesman for Egypt's interim presidency, Ehab Badawi, said in a statement ahead of the official announcement. "This vote represents a resounding rejection of terrorism and a clear endorsement of the roadmap to democracy, as well as economic development and stability."

After a campaign in which several no-campaigners were arrested and the government said participation was a patriotic duty, the poll's turnout is also seen as a significant indicator of the level of public support for the process.

According to officials, the turnout was a respectable 38.6% – higher than the 33% who voted in a referendum during Morsi's tenure, but lower than the 41.9% who turned out in a similar poll following Egypt's 2011 uprising.

Egypt's new constitution strengthens the country's three key institutions – the military, the police and the judiciary. It also gives more rights to women and disabled people, and removes certain Islamist-leaning clauses inserted under Morsi, while maintaining the principles of Islamic sharia as the main source of legislation.

But the referendum was seen less as a poll on the text's contents, and more of a vote on Egypt's current leadership.

In the build-up to the referendum, General Abdel Fatah al-Sisi, the army chief who ousted Morsi last July, hinted he would view a strong yes-vote and a high turnout as a mandate to run for the presidency later this year.

Most local media outlets joined the government in presenting the constitution's enactment as the only means of achieving stability following three years of economic hardship and political mayhem since the fall of Hosni Mubarak.

The make-or-break rhetoric was echoed by many yes-voters over the course of the two-day referendum. "I'm saying yes so that the country can rise again, and so that the people can eat," said Salah Abdel Hamid, a 63-year-old shopkeeper living on the western fringes of Cairo.

Enthusiasm for the poll seemed to contrast sharply between the country's north and south. In Upper (or southern) Egypt, turnout was noticeably down from 2012, whereas the opposite largely held true in the north. Southern Egypt has traditionally been a stronghold for Islamist groups, who almost all boycotted the poll in protest at Morsi's overthrow and at a crackdown on Islamist dissent – although it is unclear to what extent the poll's middling turnout was the result of a boycott, or just apathy.

The referendum's integrity has been challenged by opposition members and rights campaigners, who say the poll was conducted against a backdrop of fear. "The media was totally mobilised for a yes vote – and it wasn't a fair vote," said Amal Sharaf, a member of the 6 April movement, a liberal group that has opposed successive regimes under Hosni Mubarak, Mohamed Morsi, and the current government. "People were threatened not to vote no, people were arrested for campaigning for a no vote."

Up to 35 no-campaigners were arrested, claimed one opposition party claimed, who later boycotted the poll in protest. Their arrests follow the jailing of thousands of Morsi supporters, as well as dozens of secular activists, since last July.

Transparency International, an international monitoring group that sent a small delegation to observe the process, said in a statement: "Government officials openly promoted a vote in favour of the amendments; private and public media provided one-sided coverage in favour of the draft constitution; and the government harassed, arrested, and prosecuted peaceful critics, closing democratic space to promote views and debate before the referendum."