A Mozambique government-backed survey showed a 48% decline in elephant numbers from just over 20,000 to an estimated 10,300.
According to the Wildlife Conservation Society (WCS): "This decline is due to rampant elephant poaching in the country's most important elephant populations."
The hardest hit area is the Niassa National Reserve in the remote northern part of the country, with 95% of elephant deaths. The pachyderm population is now around 6,100, from an estimated 15,400.
Poachers are responsible for the decimation of elephant numbers, said Alastair Nelson, director of WCS in Mozambique.
"The major issue is one of governance. The north has always been a remote and poorly governed area, with an underlying level of corruption," he told AFP.
"Some district police and border guards are being paid off, some even rent out their own firearms."
Elephants are highly prized for their ivory, which is made into jewellery and statuettes.
On 14 May, police in Mozambique seized 1.3 tonnes of elephant ivory and rhino horn – the country's largest haul of illegal wildlife products. The cache was reported to have a street value of about $6.3 million, with rhino horn prized for use in traditional medicine in Asia.
Rhinos are now believed to be extinct in the country.
"Undoubtedly, this is a case related to poaching. Some ivory pieces still have fresh blood, a sign that some animals may have been recently killed," a police spokesman said.
The Mozambique government has been criticised for failing to stop poachers. It was only in June 2014 that a new bioversity law criminalising the killing of protected animals came into effect.
Previously, punishment for poachers was a fine for illegal possession of a weapon.
Mozambique is one of the poorest countries in the world and many are willing to risk their lives to earn money through poaching, according to Save The Rhino.
The charity says that the country suffers from high corruption and even Mozambican field rangers have been arrested for rhino poaching.
In 1900, there were 10 million African elephants - but in 2013 there were just 434,000.