Martinelli, who oversaw a public works boom and Latin America`s fastest economic growth in recent years, fled from Panama in January and is believed to be living in Miami.
Despite his initial popularity, his administration was tainted by allegations of corruption.
He now faces half a dozen different investigations including into alleged misuse of public funds, financial crimes, taking bribes and giving illegal pardons.
In the spying case, prosecutors say that Martinelli, 63, used taxpayer money and government employees to listen to calls, read messages and have activists, politicians, union members, lawyers, doctors and other civil groups followed.
Martinelli responded to the news on his Twitter feed late on Monday, saying this was the first round of a political trial.
Two of Martinelli`s former security chiefs have been arrested in the case and are awaiting trial.
In a letter posted on his Twitter feed this month, Martinelli said the accusations against him are a revenge campaign spearheaded by current President Juan Carlos Varela.
Varela, of the center-right Panamenista Party (PP), helped Martinelli win the presidency in 2009 before the two fell out acrimoniously.
Defense lawyer Rogelio Cruz said in October Martinelli was innocent of all charges, describing a provisional indictment as "crazy" and calling the process against him "Kafkaesque."
Neither the court nor prosecutors gave details on how Martinelli`s detention would be sought, given that he has not been seen in Panama for months.
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