The organisation, the Patriotic Front, said in a statement that officials identifying themselves as intelligence officers detained its deputy secretary general Romuald Yaro on March 30 at his workplace in the capital Ouagadougou.
Burkina Faso has seen numerous kidnappings of people viewed as critical of the military authorities since the junta's leader Captain Ibrahim Traore took power in a coup in 2022.
The group said it did not know the grounds for the arrest or where Yaro had been detained since.
His "arrest was carried out by individuals who introduced themselves as being on a mission for the ANR," Burkina Faso's national intelligence agency, the statement said.
"The Patriotic Front reaffirms its disagreement with these types of arrests, outside of judicial procedures, which are equivalent to enforced disappearances."
The Patriotic Front is made up of civil society organisations and political parties that are legally recognised in Burkina Faso.
While arrests and kidnappings have been frequent since Traore took power, they have accelerated in recent weeks.
The country has become caught in a spiral of violence blamed on jihadists that has spilt over from neighbouring Mali and Niger.
On Wednesday, three Burkinabe journalists who had been arrested over criticism of the military government appeared in a video shared on pro-junta social media accounts.
In the recording the three detained journalists, who appear to be inside a military barracks, said they were at the front line to "cover the reality" of the battle against jihadist attacks.
Last week, the government dissolved the Burkina Journalists' Association (AJB), a day after police arrested its president, Guezouma Sanogo, and his deputy, Boukari Ouoba.
The arrests came after Sanogo criticised "attacks on the freedom of expression and the press" in the west African country at an AJB congress.
Earlier in March, political movement SENS said five of its members including a journalist had been abducted after the group denounced civilian massacres blamed on the army and allied militias.
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