SEOUL, South Korea — The South Korean government apologized on Thursday for a security lapse that allowed a North Korean fishing boat to spend two and a half days in its waters without being noticed.

“What has been revealed so far is enough to cause deep concern among the people,” Prime Minister Lee Nak-yon said. “We offer our deep apologies.”

The 33-foot wooden boat crossed the maritime border with South Korea last week with four North Korean men on board. Neither the South Korean Navy nor the Coast Guard knew about it until Sunday morning, when the boat docked at Samcheok, a port 80 miles south of the border.

One of the four North Koreans then came ashore, telling a South Korean villager that he came from the North and asking to borrow a cellphone so he could call an aunt who had earlier defected to the South.

During an initial interrogation by the South Korean authorities, two of the four North Koreans said they wanted to defect to the South. The other two were returned to the North on Tuesday over the land border. Officials were still investigating the circumstances of the North Koreans’ travel to the South, including whether the two defectors had commandeered the ship during a fishing trip.

Defense Minister Jeong Kyeong-doo promised a thorough investigation of allegations in the South Korean news media that the military had tried to cover up its failure to detect the North Korean ship.

”The military will launch a thorough review of its vigilance and will issue stern punishment if there is anyone who should be held responsible,” Mr. Jeong said. “It will supplement its vigilance and tighten its discipline so an incident like this will not happen again.”

The government’s apology came on the same day that President Xi Jinping of China arrived in North Korea for a state visit with Kim Jong-un, the country’s leader. Mr. Xi seeks to play a mediating role in persuading Mr. Kim to return to international talks on ridding the North of its nuclear weapons.

Since early last year, South Korea has vigorously pursued a political rapprochement with North Korea, including signing an agreement with the North to lower tensions along their border, which is guarded by minefields and barbed-wire fences.

But South Koreans remain deeply worried about any breach of the border. Nearly two million troops on both sides of the border are on constant alert against possible intruders. The two Koreas remain technically at war because the 1950-53 Korean War was halted with a truce rather than a peace treaty.

North Korean fishing boats have occasionally drifted into South Korean waters after experiencing engine trouble or running out of fuel. Those on board are returned to the North unless they express a desire to defect, as five North Koreans on one boat did in 2017.

But the South Korean military has sometimes been criticized over security lapses by land or sea.

In 1996, when a small North Korean submarine ran aground with engine trouble on the South’s eastern coast, it was a taxi driver who first alerted the police. Twenty-six crewmen and armed agents spilled out of the submarine, setting off a 50-day manhunt.

Of that group, 13 were shot and killed by South Korean troops. Eleven were later found dead in a circle on a mountaintop, each with a bullet hole to the head in what South Korean investigators suspected to be executions and suicides. One was caught alive and another fled to the North. Fifteen South Koreans were also killed during the manhunt.

Two years later, a South Korean mackerel boat was the first to discover another small North Korean submarine that had become entangled in a fishing net off the same eastern coast. When South Korean officials opened its hatch, they found nine men with bullet wounds in their heads or chests.

In 2012, a North Korean soldier defecting to South Korea scaled three barbed-wire fences on the eastern land border without being detected, and then had to knock on the doors of a South Korean military barracks to get attention.

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