The payments, worth up to 20 times the value of the power they would have produced, raises serious concerns about such subsidies, which are paid for by the customer.
The six Scottish wind farms were asked to stop producing electricity on a particularly windy night last month as the National Grid was overloaded.
Their transition cables do not have the capacity to transfer the power to England and so they were switched off and the operators received compensation. One operator received £312,000, while another benefited by £263,000.
The payments were discovered by the Renewable Energy Foundation, a green think tank, which accused the Government of building too many wind farms in northern Britain.
John Constable, director of policy and research, said not enough care had been taken to ensure there were enough high-voltage cables to transfer the power to other parts of the UK when it was needed.