The International and Safety Organisation (INSO) was responding a day after the country's Security Minister Mahamadou Sana accused its staff of "spying and treason".
"We categorically reject the allegations made regarding our activities in Burkina Faso and remain committed to doing everything in our power to secure the safe release of all our colleagues," it said in a statement.
Since July, the authorities have arrested eight staff members: a Frenchman, a French-Senegalese woman, a Czech man, a Malian and four Burkinabe nationals.
The group's director in Burkina Faso is among those being held, having been detained at the end of July.
The INSO, based in the Netherlands, specialises in safety for aid workers, providing security analyses for humanitarian organisations.
Sana in his comments Tuesday, alleged the group had "collected and passed on sensitive security information that could be detrimental to national security and the interests of Burkina Faso, to foreign powers".
Despite it having been banned from operating on July 31, some members had continued operating "covertly", he added.
In its statement Wednesday, the INSO said the authorities had been "fully aware of our work and mandate.
"We have operated in Burkina Faso since 2019, following requests to support NGOs there, and we are registered with relevant ministries in accordance with local laws," it added.
"Associating our work to strengthen humanitarian safety with intelligence work is not only false but will only serve to place aid workers at greater risk," it said.
Burkina Faso's military junta has turned away from the West and in particular former colonial master France since seizing power in a September 2022 coup.
Burkinabe authorities often repress dissent, notably within civil society and the media, claiming it as part of the battle against jihadist violence that has plagued the country for a decade.
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