Metro Manila (CNN Philippines, September 26) — The government's move to void amnesty granted to opposition senator Antonio Trillanes IV does not apply to his co-mutineers, Presidential spokesperson Harry Roque said on Wednesday.

"I daresay that the fact that he is the acknowledged leader of the Magdalo mutineers is a reasonable basis for singling Trillanes out," Roque told CNN Philippines' The Source. "In effect the message that government is sending is: It's enough that we punish the leaders. We will not bother with the rank and file, but it's important to hold the leader accountable for his past acts."

Roque later added, "[He was] not singled out, but the process has been limited to him because it's important to send a message that you must comply with the requirements set by law."

The soldier-turned-senator is the subject of a controversial Presidential proclamation, which voided amnesty granted to Trillanes for his involvement in coups against former President Gloria Macapagal-Arroyo's administration. He is also a vocal critic of President Rodrigo Duterte.

A Makati Regional Trial Court issued a warrant of arrest for Trillanes on Tuesday, and he has since posted bail. But the senator still faces another pending case in a separate court, this time for the non-bailable offense of staging a coup d'etat, which was dismissed in 2011.

Meanwhile, Defense Secretary Delfin Lorenzana said court martial proceedings remain on hold, pending a warrant of arrest. The government previously said the military tribunal has jurisdiction over Trillanes' case, but the senator's camp maintains he resigned from the military when he ran for Senate.

Trillanes, a former naval officer, was involved in the Oakwood mutiny in July 2003, the Marines standoff in February 2006, and the Manila Peninsula incident in 2007. Among those alongside him were Magdalo Rep. Gary Alejano and Office of Civil Defense administrator Nicanor Faeldon.

Critics of the proclamation worry what the arrest warrant means, not just for Trillanes, but for all people who have availed or will avail amnesty.

"Kung kukuwestiyunin ang sa kanya, lahat iyon malalagay sa peligro," Senator Grace Poe remarked. "Mawawalan ng bisa ang amnestiya na ibibigay ng gobyerno sa darating na panahon. Paano magkaroon ng tiwala?"

[Translation: If (Trillanes' amnesty) is questioned, it endangers everyone else. Future amnesties granted by government will not have value. How will people believe in it?]

But Malacañang said the amnesty granted to other Magdalo soldiers still stands — at least for now.

"Unless questioned, it remains valid," said Roque.

He added that other soldiers "better have a copy of their [amnesty] application form" if they are questioned.

The government is disputing whether Trillanes even applied for amnesty in the first place, as he has not shown a copy of his application form. Trillanes' camp maintains that it is the Department of National Defense that has a copy, and he was not given a duplicate. He also showed media coverage of the day he filed the application.

RELATED: Gary Alejano: What if gov't burned Trillanes, Magdalo soldiers' amnesty applications?

Malacañang also maintained that a recent dip in trust and approval ratings for Duterte has nothing to do with Trillanes. The case of the senator came amid a nine-year inflation high, a rice crisis, and a weaker peso.

"We don't really consider Sen. Trillanes as a major hindrance to governance. He is a minor legal issue that's being addressed by a few lawyers," said Roque.

"We can't deny the rising cost of goods and services may be behind the decline in survey results. But the message that we're sending is we're doing everything that we can," he added.

The senator previously said that the government could not get away with using him as a diversion for rising prices of goods.

RELATED: Congressman: Trillanes arrest won't help ease inflation

If Trillanes is jailed, he will be the second sitting senator and Duterte critic to be detained. The first is Senator Leila De Lima, who faces what she maintains are trumped up drug charges.

While critics see the move as a way to stifle dissent, Malacañang maintains that it is not about persecution.

"[The President] wants to implement the law," said Roque. "If as a consequence of it, [Trillanes] will be detained, so be it."

CNN Philippines Senior Correspondent David Santos contributed to this report.