Bats, a local delicacy, appeared to be the "main agents" for the Ebola outbreak in the south, Rene Lamah said.
Sixty-two people have now been killed by the virus in Guinea, with suspected cases reported in neighbouring Liberia and Sierra Leone.
Ebola is spread by close contact. There is no known cure or vaccine
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It kills between 25% and 90% of victims, depending on the strain of the virus, according to the World Health Organization (WHO).
It is the first time Ebola has struck Guinea, with recent outbreaks thousands of miles away, in Uganda and the Democratic Republic of Congo.
Mr Lamah announced the ban on the sale and consumption of bats during a tour of Forest Region, the epicentre of the epidemic, reports the BBC's Alhassan Sillah from the capital, Conakry.
People who eat the animals often boil them into a sort of spicy pepper soup, our correspondent says. The soup is sold in village stores where people gather to drink alcohol.
Other ways of preparing the bats to eat include drying them over a fire.
Ebola virus disease
- Causes severe outbreaks of viral haemorrhagic fever (VHF)
- Fatality rate of up to 90%
- Occurs mostly in remote villages in Central and West Africa, near tropical rainforests
- Transmitted to people from wild animals and spreads through human-to-human contact
- Fruit bats are thought to carry the Ebola virus
- No treatment or vaccine
Certain species of bat found in West and Central Africa are thought to be the natural reservoir of Ebola, although they do not show any symptoms.
Health officials reported one more death on Tuesday, bringing the number of people killed by Ebola to 62, our correspondent adds.
The charity Medecins Sans Frontieres has set up two quarantine sites in southern Guinea to try to contain the outbreak, the Associated Press news agency reports.
Health authorities are receiving help from the WHO while messages are being broadcast on national television to reassure people.
Sierra Leone's health ministry said it was investigating two suspected cases of Ebola.
"We still do not have any confirmed cases of Ebola in the country," its chief medical officer Brima Kargbo told AFP.
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