Nominally, this would be either British or Russian depending on how you want to review the works.
According to Wiki, the original vision of Captain Nemo was that of a Polish aristocrat whose family had been killed by Russian. As the final ship was supposedly from the nation that Nemo had fought against, that would have made it Russian. However, due to political alliances (at the time France was allied with Tsarist Russia) the enemy country was changed to Britain.
This theme was later carried on in the sequel "The Mysterious Island" in which on his death bed Captain Nemo reveals his true identity as an Indian Prince Dakkar, a son of a Raja. After participating in the Indian Rebellion of 1857, Prince Dakkar escaped and commenced the building of the Nautilus with the new name of Captain Nemo. That would again make the country of origin for the mysterious ship British.
Note, in the movie adaptation "The League of Extraordinary Gentlemen" Nemo is depicted as of Indian heritage.