Since opening two years ago the museum has failed to hit visitor and income targets, and the city council has been forced to step in to support it.
The museum, which is dedicated to the city's maritime past, cost £15milion to build and opened to great fanfare two years ago.
It also had a promising first year in which it beat its visitor target by 20,000, with more than 140,000 people visiting the museum.
But visitor numbers tailed off dramatically in its second year of operation, to around 100,000, and it is currently running at a loss.
A Freedom of Information request has revealed the council was forced to pay £430,000 in subsidies since the museum opened.
That is leaving the council with a hefty bill to subsidise the museum at a time when the authority facing having to make up to £30million of cuts in the next financial year.
The cash-strapped authority has already axed more than £30million of savings and 300 jobs in the last two years.
Labour council leader Simon Letts said he was “disappointed” by the figures, but added: “We have some good exhibitions coming up that I think will boost visitor numbers, and I think the current one is excellent too.”
Conservative opposition finance spokesman John Hannides, who was leisure chief when the museum opened, said: "My concern is the budget decisions for the SeaCity were being made more around the council's desire to cut spending rather than what might be better for the museum, for example with the marketing and advertising budget.
"I would like to see the council look at outsourcing the management of the museum and bring in specialist experts with a track record of running attractions."