Officials at the Canada Science and Technology Museum say contractors discovered airborne mould this week in the facility's water-logged south wall.
The discovery, during a week of routine annual maintenance, forced the immediate evacuation of staff and prompted an indefinite closure to visitors.
Birthday parties and school-group visits are being cancelled, postponed or diverted to other facilities.
Spokesman Olivier Bouffard says the museum remains under "lockdown," and that a meeting with contractors Friday afternoon did not resolve how long repairs will last or their price tag.
"It's a complex situation," Bouffard said in an interview.
The museum is tucked inside an old bakery warehouse, bought by the federal government from a distressed company in 1967, in a shabby industrial park.
The old bakery loading docks are still visible among the science exhibits in what was to be a "temporary" home.
In July, incoming CEO Alex Benay was warned the 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 a briefing book obtained by The Canadian Press under the Access to Information Act.
The leaky roof needs to be replaced for $2.5 million, and new roof-top heating and ventilation systems are needed, at $845,000.
But the cash-strapped corporation has been able to set aside only $550,000 for all the maintenance work, much of which will likely now be diverted to the mould problem.
In the meantime, three leased industrial buildings nearby hold most of the science museum's 40,000 artifacts, or about 130 per cent of the buildings' design capacities.
To alleviate the storage pressure, harried officials have had to get rid of more than 1,000 artifacts in the last two years — "deaccessioned" is the official term — to free up space.
The poor-quality buildings "have inadequate temperature and humidity control contributing to artifacts deterioration," says the briefing book.
Attendance, meanwhile, has been falling for the last few years, accelerated by a decision to charge parking fees beginning in August 2013.
"As the building further deteriorates, the comfort and enjoyment of visitors is affected, which has been shown to lead to lower visitation and decreased revenues," says the released material.
The number of visitors has dropped about eight per cent in the last three years, to 285,000 in 2013-2014 from 309,000 in 2011-2012.
Gift shops and other commercial activities, including boutiques at the separate aviation museum and agriculture museum, which are corporately linked to the science museum, make about $1 million in revenues. But expenses of $900,000 leave net revenues of just $100,000.
A charitable foundation set up by the museum corporation is bringing in only about $150,000 annually.
For more than a decade there have been proposals to build a new science museum, costing from $300 million to $800 million, on a more central site able to capture more visitors.
But the Conservative government has been more interested in deficit-cutting since 2011, and there have been no commitments as ministers give the cold shoulder to any grand building plans.
The science museum in 2010 tried to cash in on the Conservative government's newfound interest in the Franklin expedition with its Echoes in the Ice exhibition, featuring a few artifacts from the ill-fated 19th-century effort to find the Northwest Passage.
Significantly, Prime Minister Stephen Harper chose a private display case outside his office in the Centre Block of Parliament Hill in recent years to feature relics of the Franklin expedition, rather than put them in the publicly accessible science museum.
A spokesman for Canadian Heritage Minister Shelly Glover, the minister responsible, noted that the Crown corporation that runs the science museum operates "at arm's length from the government, and is responsible for its own maintenance and repairs."
"We are closely following developments as the museum works to remedy the situation," Mike Storeshaw said in an email.
Bouffard said contractors discovered the mould this week while inspecting a seal that had to be installed in October last to prevent hazardous asbestos in the ceiling from contaminating the air.
The inspection showed the seal is working well, but also uncovered a water leakage that prompted workers to punch a hole in the south wall, where they discovered potentially toxic mould.
The Canada Science and Technology Museums Corp., which runs the science, aviation and agriculture museums, currently receives $26.5 million in annual funds for all three facilities.
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