The problem was detected earlier this month during an inspection of the facility's waterlogged south wall.
The museum was immediately closed to visitors and now the institution says it won't re-open this year.
No date has been set for a re-opening, as contractors are still assessing what needs to be done to alleviate the problem.
Staff have been moved to other facilities, including the Canada Aviation and Space Museum and the Canada Agriculture and Food Museum.
The mould invasion at the national science museum is just the latest blow to a crumbling facility that is jettisoning artifacts, postponing critical repairs and squeezing visitors for new parking fees in a bid to stay afloat.
People who had made reservations to visit or who planned activities at the museum this fall are being advised about alternative venues, the museum said.
Meanwhile, the museum corporation is working to assess the damage and plan for fixing it.
"We want to assure all those who support the museum we are working with determination towards a complete, permanent solution to this unfortunate issue," said CEO Alex Benay.
The troubled museum sits in a shabby industrial park. It is housed in an old bakery warehouse which the federal government bought from a distressed company in 1967.
A briefing book prepared for Benay when he took the top job in July warned that place is falling apart after almost 50 years of neglect.
"The corporation has come to a critical point in the replace-or-repair juncture," says the briefing book.
The leaky roof needs to be replaced at a cost of $2.5 million, and the place needs $845,000 for new roof-top heating and ventilation systems.
But the cash-strapped institution has been able to set aside only $550,000 for all the maintenance work, much of which will likely be diverted to the mould problem.