KUALA LUMPUR, Malaysia — For years, North Korea has enjoyed the freedom for its citizens to visit, work and live in Malaysia, a rare privilege for a nation considered an outlaw by most of the world.

Now that freedom is in danger, with the North Korean Embassy in a suburb of Kuala Lumpur, the Malaysian capital, at the center of a murder investigation that is upending the cozy diplomatic relationship between the two countries.

Two North Korean men accused of participating in the Feb. 13 assassination of Kim Jong-nam, the half brother of North Korea’s leader, Kim Jong-un, have taken refuge in the embassy and are refusing to cooperate with the police. Their stance is presenting the Malaysian authorities with a daunting challenge as they try to crack a case with major international ramifications.

One of the two men, Hyon Kwang-song, is a high-ranking embassy employee who claims diplomatic immunity and, as a result, is untouchable by the police. The other, Kim Uk-il, an employee of the state-owned airline, Air Koryo, is safe from arrest as long as he remains on the embassy grounds.

South Korean intelligence officials said on Monday that Mr. Hyon worked for North Korea’s Ministry of State Security, the country’s secret police.

"The embassy is considered the sovereign territory of the country concerned, so the authorities cannot enter without permission,” said Sivananthan Nithyanantham, a Malaysian lawyer who has served as counsel at the International Criminal Court in The Hague. "To do so would be akin to entering foreign soil without consent and would be a serious breach of diplomatic protocol.”

The Vienna Convention of 1961 gives diplomats and embassies a special protected status intended to safeguard the conduct of international affairs. But over the years, there have been several high-profile cases of diplomats and citizens who have sought to use these protections to avoid prosecution for serious, nondiplomatic crimes.

During a tense standoff with the United States, Gen. Manuel Antonio Noriega, the former Panamanian dictator, took refuge in the de facto Vatican embassy in Panama City in 1989 to avoid capture by United States troops who had come to seize him. He was forced to leave after 10 days when the Vatican declined to give him asylum.

And Dominique Strauss-Kahn, the former head of the International Monetary Fund, unsuccessfully sought to invoke diplomatic immunity to avoid a lawsuit alleging that he sexually assaulted a hotel maid in Manhattan in 2011. But his claim of immunity was rejected by a New York State judge because Mr. Strauss-Kahn had already left that post before the suit was filed.

One of the best-known diplomatic asylum seekers is Julian Assange, the WikiLeaks founder who has been holed up at the Ecuadorean Embassy in London for five years to avoid extradition to Sweden on accusations of rape. Although he is not a diplomat, Ecuador has granted him asylum and allowed him to stay at the embassy.

Like Mr. Assange, Kim Uk-il, the North Korean airline employee, is vulnerable to arrest should he ever leave the embassy grounds — or, in his case, if relations sour to the point that Malaysia and North Korea cut diplomatic ties and the embassy closes.

Intelligence services, including the C.I.A., routinely assign agents to work in foreign embassies in the guise of diplomats, largely because of the protections of diplomatic immunity. Governments sometimes expel these agents when espionage is uncovered. But it is rare for someone working under diplomatic cover to be linked to a murder and for a government to seek an arrest.

The police say Kim Jong-nam was assassinated by two women who rubbed VX nerve agent on his face. Siti Aisyah, 25, of Indonesia, and Doan Thi Huong, 28, of Vietnam, were charged on Wednesday with his murder. They have said they thought they were participating in a harmless prank.

South Korea has blamed the North Korean government for Mr. Kim’s assassination, and the Malaysian police have identified eight North Korean men, including Mr. Hyon, an embassy second secretary, and Kim Uk-il as participants in the plot.

North Korea said on Wednesday that the conclusion that Mr. Kim had been killed by VX nerve agent was "the height of absurdity” because such a poison is so powerful that it would have killed more than just one person.

The poisoning in the middle of Kuala Lumpur’s busy international airport has prompted some Malaysians to call for an examination of their country’s role in helping North Korea connect with the outside world — and to question whether the North should be allowed to have an embassy in Malaysia.

Dennis Ignatius, a former Malaysian ambassador to several Western Hemisphere countries, called Malaysian officials "naïve and gullible” in dealing with North Korea and questioned why the rogue state had ever been allowed to open its embassy in the first place.

He urged the government — sometimes known by the same name as its geographic location, Putrajaya — to downgrade relations with North Korea. He suggested expelling North Korea’s ambassador, revoking the visas of North Koreans working in Malaysia and closing Malaysia’s embassy in Pyongyang, the North Korean capital. Malaysia has already recalled its ambassador there for consultations.

"The real question is why Putrajaya has allowed North Korea to turn Malaysia into one of its most important bases of operation in the region from which to carry out clandestine activities, circumvent U.N. sanctions and engage in all sorts of illicit enterprises to earn hard currency for the regime,” he wrote in a blistering blog post this week.

Under the Vienna Convention, countries can declare a foreign diplomat "persona non grata.” Malaysia is said to be considering that designation for Mr. Hyon and his superior, Ambassador Kang Chol, who issued a strongly worded statement last week accusing Malaysia of colluding with South Korea in the Kim case.

Both Malaysia and North Korea have signed the Vienna agreement, which allows a country to waive immunity for its own diplomats.

This happens only rarely. Malaysia waived immunity in the case of its military attaché, Muhammad Rizalman bin Ismail, who was arrested in New Zealand in 2014 on suspicion of sexually assaulting a young woman.

He claimed diplomatic immunity and left New Zealand to avoid prosecution. But given the nature of the charges, Malaysia revoked his immunity and returned him to face trial in New Zealand, where he pleaded guilty.

In another unusual case, in 1997, President Eduard A. Shevardnadze of Georgia revoked the immunity of Gueorgui Makharadze, a high-ranking diplomat at the embassy in Washington, who was then tried and convicted in the drunken-driving death of a 16-year-old girl in Maryland.

In 2011, American officials argued that Raymond A. Davis, a C.I.A. contractor who killed two Pakistanis on a crowded street in Lahore, was entitled to diplomatic immunity, a claim rejected by the Pakistani government. He was eventually freed and left the country after the victims’ families were promised millions of dollars in "blood money.”

In Kuala Lumpur, the Malaysian government, which declined to discuss the case, could face a protracted standoff with North Korea over the two suspects in the embassy.

About 1,000 North Koreans live and work in Malaysia, where their companies have rare access to global markets and the international banking system. For their part, Malaysians can visit North Korea without a visa, but few have reason to go. With such an imbalanced relationship, Malaysia may have little to lose by severing ties with North Korea if it continues to deny the police access to the suspects.

"This is certainly one of the world’s most secretive and ostracized countries, and probably for good reasons,” said Oh Ei Sun, a former secretary to Prime Minister Najib Razak and an adjunct senior fellow at the S. Rajaratnam School of International Studies in Singapore. "We should really think twice about letting them come in freely.”

Agencies