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The bailout will come from the Government's Strategic Tourism Assets Protection Programme, which is part of its $400m package for the tourism sector.
Tourism Minister Kelvin Davis said Whale Watch Kaikōura supported hundreds of jobs and other sectors in the local economy through accommodation, hospitality, retail and other activities.
Davis said by "safeguarding this key destination tourism asset", the Government would support the Kaikōura community itself.
Whale Watch Kaikōura was one of the key tourism assets New Zealand couldn't afford to lose, said Davis.
This is the second business to get a package from the Strategic Tourism Assets Protection Programme after $4m was given to Discover Waitomo last week. A further $20.2m was given to the 31 Regional Tourism Organisations.
Applications for the programme close on Thursday, June 18.
"We will continue to work with tourism operators to protect those assets that are vital to our sector's recovery and our economic rebuild," Davis said.
According to the criteria on the Ministry of Business, Innovation and Employment, eligible businesses must:
• Have at least 25% of its output purchased by tourists or include a tourism-characteristic product, for example being an attraction, allowing access to a tourist site or provide amenities.
• Be of national, regional, cultural, environmental or historic significance with significant visitor numbers and has significant spill over benefits to its wider region.
• Have exhausted all other avenues for support and be able to demonstrate "insurmountable" costs or challenges in hibernating the business, that its dependent on visitor flows which have been severely reduced and that its facing severe financial stress.