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.

Up to 40mm (1.5in) could fall, with a yellow be aware warning in place until 22:00 BST.
Forecasters are uncertain about how heavy and persistent the rain will be.
The warning covers Carmarthenshire, Pembrokeshire, Powys, Caerphilly, Merthyr Tydfil, Neath Port Talbot, Rhondda Cynon Taff, Bridgend, Cardiff, Swansea and Vale of Glamorgan.
A moist southerly airstream is set to bring the bulk of the rain in a four-hour period, with the Met Office saying it will issue further updates to the warning throughout Monday.
It said it could lead to standing water and spray on roads, making travel conditions tricky.

The London derby will kick off at 17:15 BST on Saturday, 22 April.
Spurs are one of only four clubs to beat Premier League leaders Chelsea this season - a 2-0 victory in January.
The second Wembley semi-final between Arsenal and Manchester City, which will kick off at 15:00 BST on Sunday, 23 April, will be shown on BT Sport, with highlights later on BBC One.
Tottenham won the 1967 FA Cup with a 2-1 win over Chelsea, while the Blues beat Spurs 5-1 in a semi-final at the new stadium on their way to winning the competition in 2012.
It is the third meeting between the sides the season - Chelsea won 2-1 at Stamford Bridge in November - and Spurs will hope to have striker Harry Kane back from an ankle injury.
Football Focus will come live from Wembley on the Saturday as part of the build-up to the semi-final.
Chelsea beat holders Manchester United 1-0 on Monday to reach the semi-finals, a day after Tottenham thrashed League One side Millwall 6-0 in their quarter-final.
A rare population of elephants in northern Mali is being targeted by poachers, threatening its survival, a wildlife official has said.
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Outbreaks of heavy rain will hit parts of south, mid and west Wales through Monday, the Met Office has warned.
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The FA Cup semi-final between Chelsea and Tottenham at Wembley Stadium will be broadcast live on BBC One.