Marcelo Nieva from RÃo Tercero, Cordoba Province, was shot at multiple times, along with church member Daniel Carreño, but both men escaped unharmed.
The Pueblo Grande Baptist Church leader has previously been threatened with attack and a federal court ruled over the summer that the church should be provided with round-the-clock protection.
Pastor Marcelo regularly works with victims of domestic violence, sex trafficking and drug addicts, but he came up against the law last year when charges were brought against him under "anti-cult" legislation adopted at provincial level.
Argentinian denominational leaders and legal experts criticised the anti-cult law used to target the church, which belongs to a denomination with a 105-year history in the country.
Some believe the pastor was targeted by corrupt politicians and members of the local police force because of the church's work with victims.
A group of national church leaders in Argentina has expressed concern over the latest attack and called for more protection for him.
Anti-persecution group Christian Solidarity Worldwide has also spoken out.
Chief Executive Mervyn Thomas said: "This is the culmination of a long campaign of harassment and attacks on Pastor Nieva and his church, and we are concerned that impunity will only embolden those responsible.
"We thank the Argentinian Federal Government for the protection it has assigned to Pastor Neiva and the church, but call on government officials to do more to ensure that these kinds of attacks do not happen again.
"We also call on the government to repeal the anti-cult legislation which has been manipulated to target this pastor and church and constitutes a serious threat to freedom of religion or belief in Argentina."