The patient was a resident of the eastern Malaysian state of Sabah, the Ministry of Health said, and already was in fragile health due to heart problems, high blood pressure and other maladies.
But the case, coming two days after authorities reported the country's first case of Zika, is likely to add to fears of a full-blown outbreak of the mosquito-borne virus in the tropical nation.
The ministry said local transmission was highly likely because the man had no recent history of travelling outside Malaysia.
Ministry Director-general Noor Hisham Abdullah told state news agency Bernama his prior health problems were the cause of death on Saturday afternoon, but that the results of a full investigation were pending.
On Thursday, Malaysia reported the first Zika case on its soil -- a 58-year-old woman who is believed to have contracted it on a visit to neighbouring Singapore, where 150 cases have been confirmed.
A study published Friday in The Lancet Infectious Diseases journal said at least 2.6 billion people could be at risk from the virus in mosquito-ridden parts of Africa, Asia and the Pacific.
Zika, which is spread mainly by the Aedes mosquito, has been detected in 67 countries and territories including hard-hit Brazil.
It causes only mild symptoms for most people such as fever and a rash, but infected pregnant women can give birth to babies with microcephaly, a deformation marked by abnormally small brains and heads.
Malaysia already has struggled in recent years to control the spread of Aedes-borne dengue fever.
It has been bracing for Zika after Singapore reported a surge in cases beginning a week ago.
Malaysia has stepped up screening of travellers from abroad, particularly Singapore, and fogging with mosquito-killing chemicals while urging the public to eliminate mosquito breeding sites such as stagnant water.
A health worker carries out fogging in a Malaysian village
Malaysia reported its first locally transmitted Zika case on Saturday, a 61-year-old man who has died of heart-related complications, the government said.