Peter Dahlin, who worked for the Chinese Urgent Action Working Group, disappeared earlier this month as he prepared to board a flight to Thailand, and appears to have been caught up in a crackdown on human rights lawyers.
Late on Tuesday, state broadcaster China Central Television showed a video of him confessing that he had "violated Chinese law through my activities here".
In stilted tones, he declared: "I have hurt the feelings of the Chinese people. I apologise sincerely for this."
Dahlin's group has said it offered training to human rights lawyers who have tried to use China's tightly-controlled judiciary to redress apparent government abuses.
"I have no complaints to make," the Swede was shown saying. "I think my treatment has been fair."
Two purported Chinese colleagues of Dahlin were also shown declaring their guilt.
In China high-profile criminal suspects are regularly paraded on television apparently confessing to their actions, in what rights lawyers say is a violation of criminal procedure.
It is rare for China to accuse foreigners of national security offences, which can carry heavy penalties, although some have been accused of spying.
The EU was "deeply concerned" about cases such as Dahlin's, the grouping's ambassador to China Hans-Dietmar Schweisgut told reporters.
"We do hope it's not representing the new normal yet, but we do see an extremely worrying trend," he said.
Dahlin's case came after two Hong Kong booksellers with European citizenship vanished -- one from the former British colony and the other from Thailand -- to re-emerge in China, raising fears of Chinese authorities operating internationally.
Lee Bo, who has a British passport, and Swede Gui Minhai were both born in China and were rumoured to be preparing a tell-all book about the love life of Chinese President Xi Jinping.
On Monday, CCTV broadcast a video of Gui confessing to a drink-driving charge and saying that he did not want the Swedish government to interfere with his case.
The Hong Kong government said Tuesday that police had received information from Chinese authorities that Lee, who disappeared from the city in December, was in China.
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Chinese authorities launched a sweeping crackdown against human rights attorneys in July, detaining more than 130 legal staff across the country.
This month at least 10 were formally arrested on "state subversion" related charges after being held in secret for six months.
The official Xinhua news agency said Dahlin's group was "encouraging the masses to oppose the government".
The Swedish embassy in Beijing told the AFP news agency on Wednesday that it had "noted the reports in the media but we have nothing more to say about these".