He served with the 1st Reconnaissance Regiment during the 1971 JVP insurrection and in 1973, he attended the Defence Services Staff College in Wellington gaining his psc qualification.

[3] On January 1, 1980, he was promoted to the rank of lieutenant colonel and was appointed commanding officer of the Sri Lanka Electrical and Mechanical Engineers when fraud and robbery was reported in army workshops.

In March 1981, he was appointed commanding officer of the 1st Battalion, Sri Lanka Sinha Regiment and tasked with undertaking disciplinary action following a clash between Sinha Regiment troops and police officers of the Fort Police Station on 20 January that year.

He was thereafter appointed commanding officer of the 1st Reconnaissance Regiment, Sri Lanka Armoured Corps from July 1982 to June 1983.

In August 1989, amidst of the second JVP insurrection in the southern parts of the island, Waidyaratne was appointed concurrently as the Commander of Operation Combine with responsibility for the security of Colombo Metropolitan area.