The 3,776-metre (12,389-foot) Fuji last erupted in 1707 but geologists have included it as one of 47 volcanoes in Japan believed to be at risk of eruption in the coming century.
Despite there being no sign of volcanic activity so far, the advice will come into effect ahead of the official climbing season for the popular peak, which begins in July.
"After experiencing the eruption of Mount Ontake last year, we will strongly urge climbers to be equipped with a helmet, dust mask and goggles, in addition to a raincoat, headlight and protection gear against the cold," said a local official.
On September 27 last year, Mount Ontake, some 120 kilometres (75 miles) from Fuji, erupted without warning -- killing 56 people and leaving at least seven others missing in Japan's deadliest volcanic episode for almost 90 years.
Despite being Japan's highest mountain, Mount Fuji is a relatively easy climb that can be done in less than a day.
During July and August the trails are so packed with hikers that there are often jams while groups wait for others to pass.