The marches were illegal and no group had sought permission to hold them, police said.
Thousands of people, mostly men, lined the streets north of downtown Maputo, burning tires and looting shops as they made their way into the city centre.
Police appealed for calm and said they had made an unspecified number of arrests. Youths were blocking streets and public transport drivers abandoned their vehicles in the streets.
International food prices are at their highest in two years, the UN's Food and Agriculture Organization said Wednesday.
In Mozambique, the price of a loaf of bread rose 25 per cent in the past year to about 14 cents. Fuel and water costs also rose.
The FAO's food price index shot up five per cent between July and August, partly because of a drought in Russia that lifted the cost of wheat, it said.
The international food price surge also reflects higher sugar and oilseed prices, the FAO said.
Government blamed for high pricesIn Mozambique, critics say bad government decisions have made shortages worse and have accused producers of colluding to push prices up.
The FRELIMO party, in power since Mozambique won independence from Portugal in 1975, has been plagued by charges its government is corrupt and inefficient.
Violent protests over high costs erupted in Maputo in 2008, as well, when global food prices jumped. The government cut fuel prices after a week of clashes police and rioters that left four people dead and more than 100 seriously injured.
Read more: http://www.cbc.ca/world/story/2010/09/01/mozambique-food-prices.html#ixzz0yI7NsD8Z
A 12-year-old boy was shot in the head and left dead in a pool of blood in the street, a school textbook resting beside him and empty bullet casings nearby, an AFP correspondent said.
Six Red Cross rescue teams working around the capital and the suburb of Matola said the demonstrators were killed during separate protests over rising fuel and food prices, spokesman Americo Ubisse told AFP.
Maputo Central Hospital reported 42 patients were admitted after being wounded during the protests. One, a student, died from her injuries, the hospital said.
"We have had 42 cases at the hospital. Twenty-three were wounded by gunshots. Two are being operated on at the moment. Nineteen have wounds from physical attacks. One died," Antonio Assis da Costa, director of emergency services, told AFP.
The unrest broke out as thousands took to the streets in poor neighbourhoods on the outskirts of the city to protest against the rising prices of fuel, wheat, bread, water and electricity in the impoverished southern African country.
Protesters burned tyres to block major roads to the airport and the city's largest suburb, Matola, as mini-bus taxi drivers went on strike and some schools closed.
A witness said the dead boy had been walking toward demonstrators when police opened fire on the crowd and hit him.
"We all saw it, all of us participating in the strike. We want justice here," said 18-year-old Eunici Antonia Kiove.
State-owned Radio Mozambique reported three dead in the town of Benfica, about 15 minutes' drive from the capital.
The broadcaster said rioters had set alight cars outside a branch of the national energy company Electricidade de Mocambique. Looters were also ransacking businesses, the radio station said.
Mozambique has seen prices climb in recent months as the value of its currency, the metical, slumped against the South African rand.
The exchange rate is currently five meticals to the rand, down from a rate of 3.5 meticals to the rand this time last year, according to exchange data from South Africa's Standard Bank.
The currency slide has taken a toll on import-dependent Mozambique.
Electricidade de Mocambique on Wednesday implemented a 13.4 percent rate increase, while the state water supplier has also raised prices in and around the capital, state newspaper Noticias said.
In 2008, six people were killed in protests against public transport fare increase.