The announcement from the bloc known as ECOWAS came days after the country's military deposed President Roch Kabore.
West Africa's main regional bloc has suspended Burkina Faso from its governing bodies over this week's military coup but stopped short of imposing any sanctions.
Friday’s suspension follows the ousting of Burkina Faso's President Roch Kabore on Monday, presenting the latest test to the 15-member Economic Community of West African States (ECOWAS), which has struggled to mount an effective response to a series of coups in the region over the past 18 months.
A delegation of ECOWAS defence chiefs will travel to Burkina Faso's capital Ouagadougou on Saturday, followed by a ministerial mission a few days later, the statement said.
Heads of ECOWAS member states will reconvene for another summit in Ghana's capital Accra on February 3 to discuss the findings of the two delegations.
ECOWAS and its international allies have condemned the coup in Burkina Faso, which they fear could further destabilise a country beset by violence, but find themselves with limited leverage.
The bloc's decision to not sanction Burkina Faso contrasted with its response to coups in Mali and Guinea, with which ECOWAS member states closed borders and imposed some economic sanctions after military takeovers in May and September.
'Crisis of credibility’
Pro-democracy activists say ECOWAS is suffering from a crisis of credibility, with West Africans losing faith in regional leaders they see as manipulating the democratic process and failing to alleviate poverty or contain violence.
In opening remarks to the summit, Ghana's President Nana Akufo-Addo, the acting ECOWAS chairman, acknowledged the organisation has work to do convincing people of the benefits of democracy.
"The happenings in the region tell us that not everybody has accepted democracy as the preferred mode of governance," Akufo-Addo said.
He added that the rest of the world was looking to ECOWAS "to be firm in this matter".
Burkina Faso's coup was in part precipitated by public frustration with insecurity caused by an uprising by militants linked to Al Qaeda and Daesh.
The violence has killed thousands and displaced millions across the Sahel region in recent years.