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.

A man in his 40s was found fatally shot near the Colnbrook bypass, Slough, on Monday.
A relative said Reuben Gregory had lived with his sister Kathleen in the area for more than 50 years. It is believed they lived in a caravan.
She described them as "very, very quiet inoffensive people".
"They are just very peaceable people, living a very simple life. That's the way they have always lived, that's the only life they know."
The family member, who did not want to be named, said the siblings had been targeted 30 years ago in a burglary during which Ms Gregory was tied up.
Emergency services teams, including armed officers, found the man at 03:30 BST.
Mr Gregory, in his 70s, and Ms Gregory, in her 50s, remain in custody.
Det Ch Supt Chris Ward, of Thames Valley Police, said investigators were treating the shooting as an "isolated incident".
He added: "I must stress that this incident is not being treated as related to terrorism and there is no threat to the wider public."
On Monday, officers arrested a 48-year-old man on suspicion of burglary in connection with the incident.
The man, who is said to be local to the area, is in police custody.

Jones, 39, and Cardiff Blues pair Danny Wilson and Matt Sheratt have been added to Wales' staff for the Pacific Islands tour in June 2017.
Wales head coach and assistant Rob Howley are away with the British and Irish Lions next summer.
"Stephen will obviously get a lot out of it but I think there'll be more going the other way," said Pivac.
Jones played well over 200 matches for Llanelli and Scarlets and returned to west Wales as a backs coach in 2015 after a spell as part of Dai Young's coaching team at Wasps.
Pivac believes he has a future at international level.
"He's been identified as a coach with a lot of potential and someone I believe will be a fine international coach going forward. He's going to be world class," said the New Zealander.
"Wales are talking about playing an attacking game so I think Stephen will be able to add something there. He's taken a lot of his qualities he showed as a player into his coaching."
Jones scored 917 points in 104 appearances for Wales and played fly-half in six Test matches for the British and Irish Lions.
He is now sharing his expertise with Scarlets stand-off Rhys Patchell, a combination Pivac says is key to the team's success.
"The relationship between the two is blossoming and that's great for Welsh rugby going forward," he added.
"Technically Stephen is very very sound, tactically very switched on. We're in a pretty good place as a result of the hard work he's been doing."
Cameroon has banned all night-time public transport on roads to curb accidents caused by heavy drinking, the transport ministry says.
[NEXT_CONCEPT]
An elderly man and his sister arrested on suspicion of murder live together in "secluded" Berkshire woodland, a relative has claimed.
[NEXT_CONCEPT]
Scarlets coach Wayne Pivac says Wales will gain when Stephen Jones joins their coaching team next summer.