Founded by actor Kyaw Thu, it has handled more than 40,000 funerals, and the government even gave him land to build new headquarters last year.
Min Ko Naing, a prominent anti-government activist, said: "This association has gained the trust and confidence of the public as it helps the poor and the needy by providing free funeral service and medical treatment."
In Myanmar, local and international non-government organisations or NGOs have to register with the home ministry and relevant government ministries to officially operate in the country.
Groups are often banned because they are perceived as being too political, too independent or because they do a better job than the government at providing social services.
It was unclear whether the ban on the associations was political, since the funeral society and others said they were given "no specific reason" as to why their registrations had not been renewed.
The Engineer Association and the Construction Association were some of the other groups targeted.
Many expressed confusion about having their registrations turned down, saying they were not political groups.
"We were shocked because our association has been in existence for more than nine decades and has constantly worked for the development of Myanmar-Chinese economic co-operation,'' a Chinese businessman who refused to give his name said on behalf of the Myanmar Chinese Chamber of Commerce.