In a notice on Monday, the home ministry's Public Security Division announced that Rafiqul would be sent into retirement.
They cited his 25 years of service and said his retirement was in the 'public interest'. He will receive all the benefits of retirement, according to the notice.
Earlier that day, Hifazat's Joint Secretary General Mamunul Haque was detained after being caught with a woman, his alleged second wife, at the Royal Resort in Sonargaon.
Hundreds of activists and madrasa students subsequently stormed the Royal Resort and snatched Mamunul away from police custody.
Leaders of the Islamist group also lodged a complaint with the police on behalf of Mamunul, which was recorded by Rafiqul.
The police have arrested several Hifazat leaders in various cases after the incident. Mamunul was also arrested on Sunday.