Bogaars was instrumental in reorganising the Special Branch. Under his leadership, the Special Branch countered a myriad of threats to Singapore’s security and stability in the turbulent years leading to Singapore’s independence. When Singapore joined the Federation of Malaysia in 1963, the Special Branch became part of the Malaysian Special Branch, and Bogaars had to report to both the Singapore and Malaysian Prime Ministers. Bogaars led the Special Branch through the tumultuous years of merger to counter the communist threat, Konfrontasi and the 1964 communal riots.

When Singapore became independent in August 1965, Bogaars was appointed Permanent Secretary at the Ministry of the Interior and Defence (MID). He later served as Head, Civil Service, and held Permanent Secretary appointments to several Ministries at different points of time. He retired from the Civil Service in 1981.