Kovrig's arrest was seen by experts as retaliation over Canada's arrest of Meng Wanzhou, the chief financial officer of Chinese telecom giant Huawei, at Washington's request on allegations related to breaking Iran sanctions Spavor is suspected of "engaging in activities that harm China's national security", the Chinese news agency added.
Based in Liaoning province, which borders North Korea, he has met with North Korean leader Kim Jong Un and famously arranged some of retired NBA star Dennis Rodman's visits there.
The Canadian government had earlier reported that Spavor was missing in China after being questioned.
The Beijing News daily has reported that Kovrig, who works for the International Crisis Group think tank, was under investigation on suspicion of "engaging in activities that endanger China's national security," -- a phrase often used in espionage cases.
Huawei's Meng was released on Can$10 million (US$7.5 million) bail by a court in Vancouver on Tuesday pending a US extradition hearing.
Her case has infuriated Beijing and shaken Canada's relations with China, which is itself embroiled in a trade war with the United States.
Spavor is based in northeast China, where he runs the Paektu Cultural Exchange programme, an organisation that facilitates sport, cultural, tourism and business trips to North Korea.
He earned recognition after helping facilitate visits by former Chicago Bulls star Rodman in 2013 and 2014. Spavor has also appeared in North Korean state media photos showing him talking with Kim a few years ago.
AFP's attempts to call his two cellphone numbers were met with messages saying "powered off" or "invalid" and calls to the Paektu Cultural Exchange office went unanswered.
"We have been unable to make contact since he let us know he was being questioned by Chinese authorities," Canadian foreign ministry spokesman Guillaume Berube told AFP.
Foreign Minister Chrystia Freeland said the Canadian government had raised his case with Chinese authorities.
China's foreign ministry did not immediately respond to enquiries. Kovrig's fate is also unknown, as Chinese authorities have yet to confirm why he is being held.
His employer, the Brussels-based International Crisis Group, said he was detained by the Beijing bureau of Chinese state security Monday night, but it has not received any information since then.
China's foreign ministry spokesman Lu Kang said Wednesday that ICG was not registered in China and its employees would be "in violation" of the law if they engage in activities in the country.
Canadian officials said they were officially informed via fax early Wednesday of Kovrig's detention.
"Canada is deeply concerned about the detention of Mr. Kovrig and Canada has raised the case directly with Chinese officials," Freeland said.
Kovrig was based in Hong Kong for ICG, working on foreign policy and security issues in the region, particularly on the Korean Peninsula.
ICG closed its office in the Chinese capital after Beijing passed a law on NGOs, which came into force in 2017, to better control the activities on its soil of foreign organisations.
Friends and experts say Kovrig may have become a "hostage" and "pawn" in the three-nation feud.
"In this case it is clear the Chinese government wants to put maximum pressure on the Canadian government," Guy Saint-Jacques, the former Canadian ambassador to Beijing, told AFP.
Freeland has also indirectly criticised statements by US President Donald Trump, who said in an interview on Tuesday he was ready to intervene in the Meng affair if it helped seal a trade deal with China.
"Our extradition partners should not seek to politicise the extradition process or use it for ends other than the pursuit of justice and following the rule of law," the Canadian minister said.
Asked by Reuters if he would intervene with the Justice Department in her case, Trump had been quoted as saying: "Whatever's good for this country, I would do." Freeland said it would be "up to Ms Meng's lawyers whether they choose to raise comments in the US as part of their defence of Ms Meng." It "will be up to the Canadian judicial process, to Canadian judges, how to weigh the significance of what Ms Meng's lawyers say.