During Álvaro Uribe's second term as president, Petro encouraged debate on the Parapolitics scandal. In February 2007 Petro began a public verbal dispute with President Uribe when Petro suggested that the president should have recused himself from negotiating the demobilization process of paramilitaries in Colombia; this followed accusations that Uribe's brother, Santiago Uribe, was a former member of the Twelve Apostles paramilitary group in the mid-1990s. President Uribe responded by accusing Petro of being a "terrorist in civilian clothing" and by summoning the opposition to an open debate.
On April 17, 2007, Senator Petro began a debate in Congress about CONVIVIR and the development of paramilitarism in Antioquia Department. During a two-hour speech he revealed a variety of documents demonstrating the relationship between members of the Colombian military, the current political leadership, narcotraffickers and paramilitary groups. Petro also criticized the actions of Álvaro Uribe as Governor of Antioquia Department during the CONVIVIR years, and presented an old photograph of Álvaro Uribe's brother, Santiago, alongside Colombian drug trafficker Fabio Ochoa Vázquez.
On April 18, 2007 the Vigilance and Security Superintendency released a communique rejecting Petro's accusations concerning the CONVIVIR groups. The Superintendency said that many of the groups mentioned were authorized by the Departments of Sucre and Córdoba, but not by the Antioquia government; it also added that Álvaro Uribe, then Antioquia's governor, had eliminated the legal liability of eight CONVIVIR groups in 1997. It was also mentioned that the paramilitary leader known as "Julian Bolívar" had not yet been identified as such and was not associated with any CONVIVIR during the authorization of these groups.
Petro has frequently reported threats against his life and the lives of his family, as well as persecution by government-run security organizations. On May 7, 2007 the Colombian army captured two Colombian Army intelligence non-commissioned officers that had been spying on Petro and his family in the municipality of Tenjo, Cundinamarca. These members had first identified themselves as members of the Departamento Administrativo de Seguridad (DAS) the Colombian Intelligence Agency but their claims were later denied by Andrés Peñate, director of the agency.