According to the official website of the Sri Lanka, Sri Lanka did not have an Army Commander from 2006 to 2009 - when the final stage of Eelam war was battled. 

According to the website, General Shantha Kottegoda was the Army Commander until December 2005 and General Jagath Jayasuriya, who is presently the Chief of Staff of Sri Lankan Defence forces, had taken over the Army from him in the mid 2009!  

The website does not make any reference to the person who served as the Army Commander from 2006 to 2009. 

The three year hiatus is created by the Army's decision to "disgracefully discharge" former Army Chief Sarath Fonseka from the military service after his foray into politics. Fonseka was court-martialed by the Army and punished subsequently when it was proven that he had engaged in political activities while in military service. As part of the punishment, his name was removed from all official plaques and documents belonging to the Sri Lanka Army.