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Yep, first thing I'd heard of it was in the comments to that article. I should have fact checked, just in case, but it is a thing.
The Immigration Skills Charge, set to be introduced in April 2017, will be levied on employers that employ migrants in skilled areas. Set at £1,000 per employee per year, and a reduced rate of £364 for small or charitable organisations, it is designed to cut down on the number of businesses taking on migrant workers and incentivise training British staff to fill those jobs.
Apparently the same fee was introduced in April for non EU workers