Juan Carlos Molina, who is said to be close to President Cristina Fernandez Kirchner, has until now been a priest in the diocese of Rio Gallegos.
The president of the Pastoral Commission of the Bishops' Conference, Bishop Jorge Lozano, said Fr Molina "was doing it because of his long experience working with young people who have fallen foul of the drug scourge but he is not representing the Church in this role."
The bishop added that the appointment "was made directly by the executive power" and "no suggestions or opinions were sought" from the Church.
Last month the bishops published a document on the problem of drugs in Argentina, denouncing the "absence of the state" and suggesting the complicity of those in positions of power.
They specifically criticised the Government for failing to fill the post of director of the anti-drugs organisation, which has been vacant since March.