The EC, the executive branch of the European Union, hoisted a rectangular version of the Swiss flag, which features a white cross on a red background, outside its offices in the Belgian city.
But the official flag, unlike the ensigns of other countries, is square.
A reporter from the Swiss Broadcasting Corporation (RTS) spotted the mistake and confronted the EC’s protocol service on Tuesday.
The service immediately recognized the error with a spokesperson saying it was mistaken when it bought the rectangular flag, RTS reported on its website.
Switzerland has a hard time with its flag, given that its is the only one in the world that is square.
During last year’s Olympic Games in Sochi, the wrong (that is to say, a rectangular) Swiss flag was hoisted during the opening ceremonies.
The flag flap in Brussels occurs as Switzerland faces tough negotiations with the EU over its plans to cap immigration, an initiative backed by voters that is at odds with the freedom of movement agreement the Swiss have signed with the 28-country bloc.
Swiss President Simonetta Sommaruga met earlier this week with EC President Jean-Claude Juncker to discuss the issue over which the two sides remain far apart.
While no progress was made in the talks, a widely published photo of Juncker enthusiastically kissing Sommaruga verged on being another faux pas, as RTS's Isabelle Ory tweeted: