The Department of Justice has asked two courts to issue warrants for Trillanes' arrest and resume criminal proceedings against him.
After being booked by police, Trillanes was escorted to a nearby court and posted bail, trailed by many journalists.
Trillanes, a former navy officer, was jailed for more than seven years for involvement in at least three army uprisings, including a 2003 mutiny against then-president Gloria Macapagal Arroyo, when he and other young officers rigged part of a road in the Makati financial district with bombs and took over an upscale residential building.
On Tuesday afternoon, a police team from the National Capital Region Police Office (NCRPO), headed by the chief of police of Makati, was sent to Senate to serve the arrest warrant against Trillanes.
Trillanes a year ago appealed to the International Criminal Court to investigate killings in Duterte's war on drugs and had repeatedly accused the president of being a mass murderer and holding secret bank accounts.
Senator Antonio Trillanes IV answers questions from reporters at a news briefing outside the senator's office at the Senate in Pasay City on Thursday, September 6, 2018.
Trillanes is the second senator arrested after voicing criticism of Duterte's drug war. "Bail for temporary liberty of the accused is fixed at P200,000 per order dated February 16, 2010", the court order read.
Trillanes has insisted that his amnesty was valid and that he followed procedure, and sought help from the Supreme Court.
Legal experts and the Integrated Bar of the Philippines, the largest lawyers' group in the country, have expressed alarm over the legal moves against Mr Trillanes for offences that were cancelled by a 2011 amnesty approved by Mr Duterte's predecessor and Congress.
The senator has been fiercely critical of Duterte's drug war which has killed thousands of people and has accused Duterte of hiding wealth.
Alameda found "factual and legal bases" for the President's proclamation, thereby junking Trillanes' defense that he, indeed, applied for amnesty and complied with all the requirements, including admitting his guilt. "This [case] has nothing to do with anything except for the vengeance of Duterte and his underlings". Darkness and evil prevail in this country.
Aside from the rebellion and coup-related charges in the two courts, Mr Duterte has also ordered the military to resume an inquiry into the senator's role in the mutinies.
Amid the unfolding developments, Malacañang, for its part, urged embattled Trillanes IV "to stop the drama and allow the legal process to take its course".