The defence ministry did not give details about what powers the joint headquarters would have.
But a senior military source in Niger said Saharan states had decided to move towards running joint operations against al-Qaeda.
"We have decided to strengthen our intelligence co-operation against all forms of insecurity and, therefore, plan to move towards joint military operations against terrorism, kidnappings and the trafficking of drugs and weapons," the source said.
Mohamed ben-Madani, editor of the London-based Maghreb Review, said it would not be easy to police the region, also known as the Maghreb.
He said the move had come "too late because al-Qaeda and the Tuareg in the Maghreb have established their bases" in the region.
"They have penetrated the security services in all countries and there is very little they [authorities] can do to control [them]," ben-Madani told Al Jazeera.
Security experts say better regional co-operation is key to containing al-Qaeda in the Sahara because its fighters often evade capture by slipping from one country into another.
Spate of attacks
Greater co-operation could also mean a larger role for Algeria, the region's biggest economic and military power - a development Western diplomats say they are keen to see.
Al-Qaeda fighters last year killed a British man, Edwin Dyer, who was kidnapped on the border between Niger and Mali.
They also shot dead a US aid worker in Mauritania's capital last June, and carried out a suicide bombing on the French embassy there in August that injured three people.
Two Spaniards are believed to be in al-Qaeda's hands after they disappeared in November last year from a humanitarian aid convoy in Mauritania.
An Italian husband and wife who were seized in Mauritania last year were last week freed in Mali.
The success of the command headquarters will depend on how regional governments steer clear of the conflicts and rivalries that have in the past derailed attempts at co-operation, an Algerian security analyst said.