"We deplore the decision," EU Council President Charles Michel told a news conference following a video summit with South Korean President Moon Jae-in.
"This law risks seriously undermining the high degree of autonomy of Hong Kong and having a detrimental effect on the independence of the judiciary and the rule of law," he said.
The EU has warned of serious consequences over China's security law for Hong Kong, which democracy activists, diplomats and some businesses say will jeopardise its semi-autonomous status and its role as a global financial hub.
Both Michel and the head of the European Commission, Ursula von der Leyen, last week held a video summit with the Chinese leadership and raised the Hong Kong issue.
Following Tuesday's South Korea-EU summit, where Hong Kong was again discussed, von der Leyen said the bloc is now discussing with "international partners" any possible measures in response but did not go into details.