It comes amid a spate of deadly attacks and increasing hostility towards the presence of French troops.
Mohamed Ibn Chambas, the special representative and head of the United Nations Office for West Africa, told the body's Security Council last week that attacks in the region have increased at a rapid pace in recent years.
But the French leader added: "We need to define much more clearly the military, political and development objectives for the next six, 12 and 18 months".
The new structure, named Coalition for the Sahel, brings the G5 states, French forces and any future troops under a single command.
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Macron initially called the... "The establishment of the G5 Sahel-France Joint Staff as part of the global coalition for the Sahel will allow our armies to grow in strength and reap convincing results in the fight against terrorism", said Kaboré.
The government of Niger declared three days of mourning after 89 soldiers were killed in an attack by suspected terrorists on a base located in the country's west, a spokesman said.
Despite the French presence and a 13,000-strong United Nations peacekeeping force dubbed MINUSMA in Mali, the conflict that erupted in the north of that country in 2012 has since spread to its neighbours, especially Burkina Faso and Niger.
"France needed to raise the stakes and stage a spectacle to show that its troops are deployed at the request of the African governments", said Judd Devermont, director of the Africa programme at the Centre for Strategic and International Studies.
"If the Americans were to decide to leave Africa it would be really bad news for us", Macron said.
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Groups allied to both the Islamic State group and al-Qaeda are active in Niger.
Military campaigns by armies in the Sahel, a semi-arid swathe of land beneath the Sahara, have also been marred by human rights abuses, which analysts say have pushed some civilians into the arms of the militants.
French troops were hailed as heroes in 2013 for helping to prevent the insurgency from reaching the capital Bamako.
Macron ordered a review of the Barkhane operation after the Mali helicopter disaster, saying "all options are on the table", implying a potential drawdown of French troops.
Salif Keita, one of Mali's most popular singers, urged President Ibrahim Boubacar Keïta in a Facebook video previous year to stop "subjecting yourself to little Emmanuel Macron - he's just a kid".
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New Zealand paceman Neil Wagner also recently made it clear he was a four-day sceptic. But I love five days only because I'm boring and don't like to change much".