The clock is ticking for Mali as it scrambles to organise key elections in less than 40 days following a ceasefire deal between the government and separatist Tuareg rebels.

The agreement, reached on Tuesday after 10 days of tense negotiations, will enable Malian troops to enter the Tuareg-held city of Kidal in the northeast to secure polls scheduled to take place on July 28.

Malians have welcomed the truce but there are fears the deal will be difficult to implement and could unravel after the vote.

Malian military sources say the accord envisages the army entering the regional capital "without delay", accompanied by French soldiers and troops from the African-led International Support Mission to Mali (AFISMA).

French President Francois Hollande told a meeting of his cabinet the agreement was "a major breakthrough" and "an important signal for the whole of Africa", his spokesman said.

But analysts raised a number of problems with securing a long-term ceasefire, including difficulties in monitoring any disarmament and differentiating Tuareg militants from the diverse range of insurgents infesting Mali's north.

"Ultimately, this is an interim agreement to allow the organisation of the presidential elections in Kidal. It has not solved all the problems, it just put off some of the problems," Malian analyst Mamadou Samake told AFP.

"The agreement has not brought about the disarmament of the Tuareg rebels. Even if we talk about confining them to camps, it would be difficult to monitor," he added.

The Malian government signed the accord with the National Movement for the Liberation of Azawad (MNLA) and a smaller Tuareg group in Ouagadougou, capital of neighbouring Burkina Faso.

The two sides agreed to halt hostilities and organise peace talks after the election but the Tuaregs were not pressed to lay down their weapons.

"It was that or nothing, but we were heading for disaster if we hadn't been able to get an agreement on presidential elections in the Kidal region," said an aide of President Dioncounda Traore.

The Tuareg occupation of Kidal has been a major obstacle to holding the election, seen as crucial to Mali's recovery from the conflict of the past 15 months.

Malian officers staged a coup in March 2012 but the weak army was overpowered by the MNLA, which seized key northern cities before being sidelined by its Al-Qaeda-linked allies.

The MNLA sided with a French-led military intervention which reclaimed most of the lost territory from the Islamists but the rebels have been reluctant to allow government troops into their Kidal bastion for the vote.

According to Samake, the biggest issues in dealing with Mali's Tuareg separatist movement "are for later", however.

"After the presidential elections, the legislative elections loom on the horizon. Former Tuareg rebels will certainly want to stand," Samake said.

"But for now, they cannot because of an arrest warrant against them. Their papers will certainly be invalidated. That could create problems."

While the arrest warrants look likely to be dropped, the accord does state that international investigators will look into crimes against humanity and war crimes committed during the conflict.

Confronted with these problems, an official from the Ministry of Territorial Administration would only say: "Let's take each day as it comes."

Meanwhile the logistics of the disarmament itself remains a fly in the ointment for all parties working for the return of lasting peace in the Kidal region.

"DDR (disarmament, demobilisation and reintegration) is a long process. It can last several months," said an AFISMA member.

Meanwhile a larger challenge exists, military sources say, in the shape of Islamist insurgents who continue to hide out in northern Mali and could launch attacks which might be wrongly attributed to former Tuareg rebels.

"We are the military -- we don't do politics," a battalion commander from a neighbouring country's army told AFP in the northern city of Gao.

"But just so there is no ambiguity, there will have to be some kind of mechanism in Kidal to prevent any infiltration of terrorists, otherwise it could complicate things."