The flag is absent from the Foreign Ministry's website under Germany's "One China policy", a decision Taiwan says it is "unable to accept".
Germany has denied reports that the flag of Taiwan has been "suddenly removed" from the website of its Foreign Ministry.
Taiwan's webpage on Germany's online listings for bilateral relations was on Wednesday accompanied by a white square, rather than the territory's flag.
Meanwhile, the flags of other countries and territories, including China's Hong Kong special administrative region, are displayed.
`Reports of the change came after German Foreign Minister, Heiko Mass, spoke about future relations between China, Germany, and the European Union.
Some on social media insinuated that the white square represented "the international symbol for surrender" towards China.
But Germany has denied that the flag was suddenly removed or replaced.
An update published by Taiwan News has since corrected their story, shown in this picture, saying that the flag does not appear to have been displayed on the site "for some time".
"Not shown on the homepage in the past"
"The flag used in Taiwan is not shown on the web pages of the German Foreign Office," a spokesperson for the German Foreign Ministry confirmed to Euronews.
The Ministry also said that, as far as can be reconstructed, the flag was not shown previously on their website either.
"It was also not shown on the homepage in the past," a Foreign Ministry spokesperson said, denying that any 'exchange' or 'removal' had taken place.
Euronews analysis using Wayback machine shows the flag of Taiwan was not present on the German Foreign website as early as November 2011.
The recent removal was also denied by the German Institute Taipei, Germany's de facto embassy in Taiwan, on Facebook, which added that the "flag's location remains blank due to technical factors."
"I think I can already rule out that this is a current change," said Rainer Breul, a deputy spokesperson for the Foreign Ministry, during a press conference on Friday.
Absence due to 'One China' policy
Germany's Foreign Ministry says that the absence of Taiwan's flag on its website is a reflection of the country's "One China" policy.
Germany, like a number of other countries, diplomatically recognises only the People's Republic of China as a sovereign state.
It does not maintain relations with Taiwan, according to the foreign office's website, which China claims as part of its territory.
The symbolic appearance of Taiwan's flag would, therefore, have huge political significance, and appear to contradict this policy.
But in a statement to Euronews, the Ministry of Foreign Affairs in Taiwan said they were "unable to accept such a difference because the page introducing Taiwan was inconsistent with other countries or regions.
"[This] will only cause unnecessary misunderstandings to the people of all countries."
This disquiet was also expressed on Facebook by Shieh Jhy-wey, Taiwan's representative to Germany.
Euronews has reached out to the German Foreign Ministry for further comment on its policy.