During 1994-99, Torrijos was appointed as the Deputy Minister of the Interior and Justice of Panama, when Ernesto Pérez Balladares was serving as the President of the country. In his capacity as the deputy minister, Martín passed a law that would privatize the industries providing wastewater services and drinking water to the people.
The law passed by the deputy minister was unsuccessful, thus the 'Democratic Revolutionary Party', founded by his father, political leader Omar Torrijos, reverted the laws as per the old system.
While Martín served as the deputy minister, crimes increased in the country and there were numerous cases of worker union riots.
A constitutional poll was held towards the end of Balladares' term as President, to decide if he would get a second chance at the elections. Majority of the members decided against it, and the young Torrijos was asked to take part in the 1999 elections.
In the elections, he contested against Mireya Moscoso, who was a member of the Panamanian 'Arnulfista Party', and wife of former President Arnulfo Arias. Moscoso, who promised to look into issues related to poverty, education and privatization of industries, won by a large margin of votes.
In 2004, Martín contested once again in the presidential elections with aims of establishing a democratic form of government and starting free trade with the United States. He was supported by his comrade Ruben Blades, who was also a famous Panamanian musician.
This time the politician was contesting against former President of Panama, Guillermo Endara, who belonged to the 'Solidarity Party'. In his campaign Endara alleged that the PRD was maintaining connections with former Panamanian dictator and US prisoner Manuel Noriega. Despite spreading allegations, Endara lost to Martin in the elections.
In May 2005, at the beginning of his term as President, Torrijos caused agitation amongst the masses, when he declared plans of repaying all foreign debts by increasing the age of retirement and the payment towards pension.
Widespread protests led by students of the 'University of Panama' ensued after this proposal made by Martín, and finally the President postponed his plans for the future.
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Since most of the public had lost their faith in the president, his plans of expanding the Panama Canal to allow more ships to pass, had to be shelved till the next year. In April 2006, he put forward his plan for the 'Panama Canal Expansion Project', which won the approval of the public, after a poll was held.
In November 2006, the President of Panama organized an international conference in his country to discuss the independence of Puerto Rico. This summit, called 'Latin American and Caribbean Congress in Solidarity with Puerto Rico's Independence' involved over two-hundred delegates from across North and South America,
Towards the end of the year, Colombian President Álvaro Uribe Vélez suggested to the Panamanian leader that a road could be built through the forest of ‘Darién Gap’, to connect the two countries. However, Martín opposed the idea vehemently, since it would not be financially, as well as environmentally viable.
On June 28, 2007, Torrijos signed the 'Panama–United States Trade Promotion Agreement' with US President George Bush, enabling free trade the two nations. Three months later, this treaty was withheld, after González Pinzón, a member of the PRD, was charged by the US court with the murder of US army sergeant Zak Hernández.
Following the legal charges, the Panamanian president asked his colleague Pinzón to step down, since the US congress had refused to go ahead with the pact.
In 2009, even though Torrijos had eventually earned the trust of his citizens, he could not contest the elections for a consecutive term as the legislature of his country prohibited him. Balbina Herrera, a fellow PRD candidate participated, but lost the elections to business tycoon Ricardo Martínelli.
Ricardo, the next President ensured that the pact for free trade was once again initiated under his leadership, in 2012.
Torrijos is presently serving as Deputy in the Central American Parliament of Panama. He is a representative of the 'International Advisory Board' of the 'Global Center for Development and Democracy', and is also the Vice-President of the 'Permanent Conference of Political Parties of Latin America' ('COPPPAL').