Wong, 22, had arrived late Monday in the German capital, where he met German Foreign Minister Heiko Maas at an event hosted by daily newspaper Bild -- a meeting China branded "disrespectful".
"The ambassador was summoned in Beijing by the foreign ministry," China's ambassador to Germany Wu Ken told reporters, without giving details.
"What I can say is how big the disappointment is on the Chinese side, and we protest very strongly. This incident will have a very negative impact on the bilateral relationship".
China has regularly accused "external forces", notably the United States, of being behind the unrest in Hong Kong.
Millions have taken to Hong Kong's streets over the last 14 weeks in the biggest challenge to China's rule since the city's handover from Britain in 1997.
Wu accused "some radicals" of using democracy as a mask to hide their separatist intentions.
But speaking earlier Wednesday at a press conference, Wong denied being a separatist, saying he simply wants free elections for the former British colony -- a promise enshrined in the 1997 handover agreement between Britain and China.
'Hong Kong people deserve democracy'
Hong Kong is the new Berlin, the young activist said, alluding to the German capital's divided past where protesters brought down the Wall separating a communist East and a democratic West.
"Three decades ago, no one expected the Soviet Union would fall. No one predicted the Berlin Wall will fall. With our pressure and determination we just hope to let the world (be) aware that the Hong Kong people deserve democracy.
"Some brand me as a separatist. But just let me make it clear: Hong Kong is asking for election system reform. We just hope to elect our own government. We just hope to elect the chief executive of Hong Kong," he told journalists in Berlin.
China has repeatedly warned it will not tolerate any move towards independence for Hong Kong, threatening to crack down hard on any "separatist" groups.
Wong pointed to pledges made in the Hong Kong handover agreement.
"Before 1997, Beijing promised to let the Hong Kong people enjoy the right of free election... so we will continue our fight until the day we enjoy democracy," he vowed.
Hong Kong was returned to China in 1997 under a handover agreement that guaranteed the territory certain levels of autonomy and freedoms unseen on the Chinese mainland.
That "one country, two systems" status persists but there are increasing criticisms of Beijing policies in the city, with accusations it is trying to muzzle criticism and keep opponents out of the territory's legislature.
''Human rights and freedom'
Wong's visit to Germany came on the heels of German Chancellor Angela Merkel's visit to China, where she stressed on Friday that the rights and freedoms of the people of Hong Kong "must be guaranteed".
Addressing the German parliament on Wednesday, Merkel said she pointed out during her trip that human rights is "indispensable for us".
Wong acknowledged that China's economic might may make world leaders hesitate about speaking out forcefully in favour of the protesters.
But he stressed that "we're not seeking any world leaders or any countries to interfere in Hong Kong's process but it's a must for the free world to support Hong Kong's democratisation".
Statements are not enough, he said, urging concrete action from the West.
German and other European countries should require a human rights clause included in any trade deals with China.
And Washington should pass a bill expressing support for the pro-democracy movement, he added.
Such a law could undermine Hong Kong's special US trade privileges by mandating regular checks on whether authorities were respecting the Basic Law that underpins the city's semi-autonomous status.
Wong will travel to the United States on Friday, where he will seek "bipartisan support" for his cause.
"I'm not sure how many days months or years it would take for us (to obtain) democracy and freedom.
"I hope one day, not only Hong Kong but also mainland China people can enjoy human rights and freedom."