The incident occurred as the Swiss National Bank (SNB) held its annual general meeting in Bern, the Blick newspaper reported.
An unidentified woman sprayed the message 'please remember why we founded you' on the billboard in red paint.
According to the paper, the protestor was campaigning in support of the campaign for monetary reform, which goes to a nationwide vote in June.
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Known as the Vollgeld Initiative in German and the Initiative Monnaie Pleine in French, the initiative calls an end to traditional bank lending and for the SNB to be the only financial institution able to issue money.
The SNB opposes the sovereign money initiative.
With the help of other activists, the spray painter removed the words a short time later.
Almost exactly one year ago an 86-year-old woman was arrested after spraying an anti-war message outside the SNB in a case that drew worldwide attention.
The peace activist spray-painted ‘Money for weapons kills' on the billboard.
She was campaigning on behalf of the Group for a Switzerland without an Army (GSsA) which had launched a popular initiative to ban Swiss financing of any company that produces arms.
If it gathers the required 100,000 signatures by October 2018, the issue will go to a national referendum.