CEO Kevin Crutchfield and president Paul Vining received $500,000 upfront and the rest will be paid over two years, on the condition they stay with the embattled firm.

The agreement is outlined in Alpha's 10-K filed with the US Securities and Exchange Commission last week.

The bonuses have been criticised by both Greenpeace and SNL Financial.

Crutchfield has been CEO since 2009 and Vining has held the presidency since 2012.

"The committee and board recognised the challenges ahead for the company and determined that the retention bonuses were necessary to retain the company’s two top executives who are critical to the company’s execution of strategic priorities given current and anticipated market and business conditions," the SEC filing read.

Retention bonuses are the tip of the iceberg for Alpha’s spending, having been ordered to pay $US27.5million in damages to the Environmental Protection Agency for more than 6000 violations.

The company must also spend an additional $200 million on wastewater treatment systems and upgrades to reduce pollution from coal.