Former Impala Platinum CEO and current Coal of Africa chairman David Brown will become interim CEO until a permanent successor is found.
Wallington has been the CEO of the company since May 2010.
In a statement released on Tuesday, Brown said Wallington had been instrumental in enabling the company to overcome a variety of regulatory challenges since the beginning of his tenure.
"On behalf of the board, I would like to thank John for his commitment and contribution in what has been a difficult and challenging period for the company and wish him well for the future,” Brown said.
“John has effectively established sound relations with the relevant government departments and civil society and a resilient management team that is equipped to take [the company] from an exploration to a mining company."
Coal of Africa corporate affairs executive director Professor Alfred Nevhutanda has also tendered his resignation from the board with effect from April 30, 2013.
He joined the board on February 2, 2009.
“On behalf of the board, I would like to thank Professor Nevhutanda for his continued dedication in establishing the company’s stakeholder structures in the areas we operate, particularly in the Limpopo province where the key coking projects which include Makhado are located,” Brown said.
“These changes will enable the company to continue to remain focused on the key organisational processes to enable it to migrate to a world-class producer of coking and thermal coal.”