The vessel, known as the VerhalenArk - or Ark of Noah - struck yachts and other boats when it came free from its mooring at Urk in the Netherlands.
Owner, Aad Peters, told local radio station Omroep Flevoland: "We have been on the road for years and have experienced many storms, but this has never happened before."
en daar gaat de ark @weermanrobert @OmroepFlevoland #storm pic.twitter.com/SAwDDZawgF
— wildrik stoffer (@WildrikS) January 3, 2018
Several people on board the four-story vessel, which measures 70 metres long and ten metres wide, had to be rescued by emergency services.
Gusts of more than 110 kilometres-per-hour were recorded in parts of the Netherlands on Wednesday as Storm Eleanor swept across continental Europe with deadly force.
Thousands of people were disrupted when hundreds of flights were cancelled at Schiphol airport in Amsterdam, while several major roads and railways were shut.
Marketed as Europe's "first floating Bible museum", the exhibit opened to the public at the November and was due to stay in Urk until the end of next month.