The latest detention comes amid a growing dispute between both countries following the arrest of a senior Chinese telecom executive earlier this month.
Officials say they do not believe this case is linked to that of two other Canadians recently held in China.
Canada says it is currently seeking more details on the detention.
Former diplomat Michael Kovrig and businessman Michael Spavor were both taken into custody in China shortly after the arrest of Huawei executive Meng Wanzhou, at the request of the US, in Vancouver on 1 December.
Mr Trudeau said on Wednesday that “we suspect the case is very different from the first two cases”, referring to the circumstances surrounding Mr Kovrig and Mr Spavor’s detention.
“We are still very much in the situation of collecting more information on this,” he said, suggesting the third Canadian was detained on more “routine” issues.
Mr Kovrig and Mr Spavor are being held on accusations of harming national security. Canadian diplomats were granted consular access to both men last week.
China has denied that the detention of Mr Kovrig and Mr Spavor is tied to Ms Meng’s arrest, but many analysts believe it was a tit-for-tat action.
Beijing had threatened unspecified consequences if Ms Meng was not released.
Canadian officials have offered no further information on the third individual detained, citing privacy laws. Consular officials are providing assistance to the individual’s family.
Ms Meng has been granted bail but may face extradition to the US on charges of violating American sanctions on Iran through Huawei’s business dealings. She denies the allegations.