About 1,250 people died in road accidents last year, the ministry said.
The decision has been strongly criticised by many Cameroonians, who say it will affect their businesses and nightlife.
The ban means that buses and taxis must be off roads from 2000 GMT to 0400 GMT.
The ministry said night travel accounted for 35% of accidents, even though few people commuted at night.
The accidents were caused mainly by heavy drinking, it said.
About 12,000 people died last year in road accidents in Cameroon and another 12,000 were wounded, the ministry said.
The BBC's Randy Joe Sa'ah in the capital, Yaounde, says that while many people welcome moves to reduce fatalities, they believe poor roads are the main cause of accidents.
Only about 20% of Cameroon's roads are tarred, he says.
Many people are not sure how they will travel to and from work because some journeys last more than six hours, our reporter says.
Police have been ordered to pull off buses and taxis that travel after 2000 GMT, raising the prospect of commuters sleeping on the roadside or walking home, he says.
The ban has also been condemned by owners of bars and night clubs, who believe that it will ruin their businesses and destroy nightlife in big cities.
Small-scale traders said their income would be badly affected because their produce would not reach markets early in the morning.
"I'm finished. This is bad for me and my children," a vegetable hawker, Grace Teboh, was quoted by the AFP news agency as saying.
Cameroon has banned all night-time public transport on roads to curb accidents caused by heavy drinking, the transport ministry says.