"This abhorrent act, effectively holding our citizens hostage, is in total disregard of all international law and diplomatic norms," Malaysian Prime Minister Najib Razak said in a statement.
In response, Malaysia announced no North Koreans would be allowed to leave their country either. Both countries have already expelled their respective ambassadors.
But North Korea and Malaysia weren't especially diplomatically close even before the killing of Kim Jong Un's half-brother.
"They had a very good relationship -- I think Malaysians are just normal, friendly, and trying to maintain a working relationship with North Korea," said Jong Kun Choi, Associate Professor of the Yonsei University Political Science and International Studies Department.
"You don't want to call it a friendship ... From the southeast Asian states' perspective is North Korea critical? No, not really."
A special relationship?
Official relations between North Korea and Malaysia were initiated in June 1973
, after China, Vietnam, Cambodia and Indonesia, but in some ways the two countries have seemed unusually close.
Malaysia is one of fewer than 30 countries to have an embassy in Pyongyang, and it's also the only country whose citizens can enter North Korea without a visa
Andray Abrahamian, associate director of research at the Choson Exchange, an NGO working in North Korea, said Malaysia's visa-free status spoke to their diplomatic competence, rather than any closeness with Pyongyang.
"For a country of its economic development, (Malaysia's) passport is surprisingly powerful ... Part of their image is their openness and they didn't see fit to exclude the DPRK from that," Abrahamian said.
There is little indication Malaysians are taking special advantage of their visa-free status. Local media in Malaysia reports that some travel agents in the country don't even offer North Korean tours, due to lack of interest
In the past, Kuala Lumpur has hosted informal meetings between the United States and North Korea, said John Delury, associate professor at Yonsei University Graduate School.
"But those meetings are held in other locations around the world, in Europe, sometimes in China ... I wouldn't say those meetings would stop because of problems with Malaysia," Delury said.
Few countries ever
Even trade between the two countries hasn't been especially strong.
According to United Nations trade data
, Malaysia exported only US$2 million of goods to North Korea in 2014, mostly medical supplies and packaging. In comparison, China sent almost US$3.5 billion.
Malaysia imported less than US$200,000 of North Korean goods in the entire year.
"(Still) I would guess Malaysia is in North Korea's top 20 (trade partners) and that's the state of North Korea's trading relationships right now," Abrahamian said.
Abrahamian said North Korea's chaotic trading methods have made building connections hard for Malaysian businesses.
"It's just all very ad hoc ... I actually spoke to a Malaysian businessperson who was working a little bit in North Korea. He said he sent them a couple of containers of food products and it went really well and they got paid," he said.
"(Then) he didn't hear from him for six months, despite multiple attempts at getting in touch."
Would North Korea risk it?
South Korea has accused its northern neighbor of the assassination. In response, North Korea's state news agency KCNA issued an angry denial to the claims, accusing South Korea of "spreading wild rumors."
It also lashed out at Malaysia for "picking on" North Korea and accused the Malaysian police of "deciding the direction of their investigation under someone else's order with no objectivity and fairness."
If North Korea did attempt a public assassination with diplomatic consequences, it wouldn't be the first time. In 1983, North Korean agents set off a bomb in Yangon
in an attempt to kill then-South Korean President Chun Doo Hwan.
It killed more than 20 people, though Chun escaped. In response, Myanmar broke off relations for more than a decade. There are suggestions it may do the same now with Malaysia.
"North Korea had a pretty significant relationship with Myanmar, I would say more important than its current relationship with Malaysia and it completely squandered that relationship in order to try to assassinate the South Korean president," Delury said.
Professor Jong said if the assassination was proven to be committed by North Korea, it could lead to the severing of diplomatic relations between the two countries.
"(If proven) it's essentially a violation of Malaysian sovereignty ... North Korea might value the killing of Kim Jong Nam much more than the bilateral relationship (with Malaysia). But it's speculation at the end of the day," he said.