Authorities believe 19 Gourma elephants have been killed for their tusks in the past month. There are estimated to be just 350-500 of the group left.
Poaching has been linked in the past to rebel groups in the region, who have connections to smuggling rings.
The Gourma elephants migrate around 600km (370 miles) a year to feed.
Because of the sparse vegetation in northern Mali they have a long-distance migration pattern that runs into Burkina Faso and Niger.
On Tuesday, Colonel Soumana Timbo of the government's nature conservation division asked MPs to provide military support to protect the species.
Mr Timbo told the BBC that the small number of rangers assigned to the region were already risking their lives.
"In the Gourma zone there is total insecurity. We have about 10 rangers covering about 1.25 million hectares, so it's quite insufficient," Mr Timbo said.
"If we send out two rangers on a motorbike they are risking their lives. So we really need joint patrols - military and rangers - and we need to focus all our efforts on stopping this massacre."
Northern Mali has been a flashpoint of conflict since Mali's independence from French rule in 1960, with the Tuareg rebels campaigning for independence or more autonomy.
The region has been further destabilised by the emergence of jihadi groups including al-Qaida in the Islamic Maghreb (AQIM), which has targeted both the government and the rebels.
In its own attempt to combat poaching, South Africa has appointed a panel of experts to examine the viability of a legal rhino horn trade,
Levels of poaching have risen to record levels in South Africa. The country is thought to be home to around 20,000 rhinos, around 80% of the worldwide population.
There were 1,215 rhinos killed in South Africa in 2014, a 21% increase on the previous year, officials say.
The 21-member panel will examine whether a legal trade in rhino horn may reduce the number of animals targeted by poachers.
"It is important to emphasise that South Africa has not taken a position on the issue and will not do so until the committee has completed its work and presented its findings," the environment ministry said in a statement.
A rare population of elephants in northern Mali is being targeted by poachers, threatening its survival, a wildlife official has said.