ISTANBUL — Turkish President Recep Tayyip Erdogan won a historic referendum Sunday that will greatly expand the powers of his office, although opposition parties questioned the outcome and said they would challenge the results.

With 99 percent of the ballots counted, the “yes” vote stood at 51.37 percent, while the “no” vote was 48.63 percent, according to the state-run Anadolu Agency. The head of Turkey’s electoral board confirmed the “yes” victory and said final results will be declared in 11 to 12 days.

Although the margin fell short of the sweeping victory Erdogan had sought in the landmark referendum, it could nevertheless cement his hold on power in Turkey and is expected to have a huge effect on the country’s long-term political future and its international relations.

The 18 constitutional amendments that will come into effect after the next election, scheduled for 2019, will abolish the office of the prime minister and hand sweeping executive powers to the president.

In his first remarks from Istanbul, Erdogan struck a conciliatory tone, thanking all voters no matter how they cast their ballots and calling the referendum a “historic decision.”

“April 16 is the victory of all who said ‘yes’ or ‘no,’ of the whole 80 million, of the whole of Turkey,” Erdogan told reporters in address that was televised live.

But he quickly reverted to a more abrasive style when addressing thousands of flag-waving supporters in Istanbul.

“There are those who are belittling the result. They shouldn’t try, it will be in vain,” he said. “It’s too late now.”

Responding to chants from the crowd to reinstate the death penalty, Erdogan said he would take up the issue with the country’s political leaders, adding that the question could be put to another referendum if the political leaders could not agree.

Opponents had argued the constitutional changes would give too much power to a man who they say has shown increasingly autocratic tendencies. Opposition parties complained of a number of irregularities in the voting, and were particularly incensed by an electoral board decision announced Sunday afternoon to accept as valid ballots that did not bear the official stamp.

“The Supreme Electoral Board changed rules midgame, after the ballot envelopes were opened, in a way contrary to laws,” said Kemal Kilicdaroglu, head of the main opposition People’s Republican Party. Earlier, the party’s vice chairman, Erdal Aksunger, said it would challenge between 37 and 60 percent of the ballot boxes and accused Anadolu’s results of being inaccurate.

But electoral board head Sadi Guven defended the decision.

“There is no question of changing the rules in the middle of the game,” he said.

The pro-Kurdish opposition party, which also opposed the constitutional changes, said it plans to object to two-thirds of the ballots.

More than 55 million people in the country were registered to vote, while another 1.3 million Turks cast ballots abroad. The ballots themselves included “yes” or “no” options but not the referendum question itself — it was assumed to be understood.

The changes will allow the president to appoint ministers, senior government officials and half the members of Turkey’s highest judicial body, as well as to issue decrees and declare states of emergency. They set a limit of two five-year terms for presidents and also allow the president to remain at the helm of a political party.

Erdogan and his supporters had argued the “Turkish-style” presidential system would bring stability and prosperity in a country rattled by a failed coup last year and a series of devastating attacks by the Islamic State group and Kurdish militants.

But opponents fear the changes will lead to autocratic one-man rule, ensuring that the 63-year-old Erdogan, who has been accused of repressing rights and freedoms, could govern until 2029 with few checks and balances.

Eager voters lined up at one Istanbul polling station before it opened at 8 a.m.

“I don’t want to get on a bus with no brake system. A one-man system is like that,” said Husnu Yahsi, 61, who added that he voted “no.”

In another Istanbul neighborhood, a “yes” voter expressed full support for the president.

“Yes, yes, yes! Our leader is the gift of God to us,” said Mualla Sengul. “We will always support him. He’s governing so well.”

Erdogan came to power in 2003 as prime minister and served in that role until becoming Turkey’s first directly elected president in 2014.

The referendum campaign was highly divisive and heavily one-sided, with the “yes” side dominating the airwaves and billboards. Supporters of the “no” vote have complained of intimidation, including beatings, detentions and threats.

Erdogan survived the July coup attempt, which he has blamed on his former ally and current nemesis Fethullah Gulen, an Islamic cleric living in the United States. Gulen has denied involvement.

Still, a widespread government crackdown has targeted followers of Gulen and other government opponents, branding them terrorists. A state of emergency has been imposed.

About 100,000 people — including judges, teachers, academics, doctors, journalists, military officials and police — have lost their jobs in the crackdown, and more than 40,000 have been arrested. Hundreds of media outlets and non-governmental organizations have been shut down.

Turkey has also suffered renewed violence between Kurdish militants and security forces in the country’s volatile southeast, as well as a string of bombings, some attributed to the Islamic State group, which is active across the border in Syria.

The war in Syria has led to some 3 million refugees crossing into Turkey. Erdogan sent troops into Syria to help opposition Syrian forces clear a border area from the threat posed by Islamic State militants.

Meanwhile, Turkey’s relations with Europe have been increasingly tense, particularly after Erdogan branded Germany and the Netherlands as Nazis for not allowing Turkish ministers to campaign for the “yes” vote among expatriate Turks.