Eight army officers are among the 25 detained soldiers, senior military sources said on Thursday.
Among those being questioned are two lieutenant-colonels and all but one of the group are from the elite Army Scout Rangers, the sources said.
Brigadier General Danilo Lim, their former commander, was removed from his post on 24 February accused of involvement in the alleged plot against Gloria Arroyo.
General Hermogenes Esperon confirmed that some members of the First Scout Ranger Regiment were being questioned but would not say how many.
"We could not tell you how deep their involvement is as that is the subject of the ongoing investigation," he said in an interview with ABS-CBN television.
Amnesty International, the London-based human rights group, called on the government to tell its security forces that extra-judicial killings will not be tolerated.
Amnesty said in a statement that comments by senior government officials linking leftist groups directly to communist insurgents threaten to "create a climate within which further political killings may take place".
"In order to combat impunity, the authorities must also send a clear, unequivocal message to all members of the police, military and other security forces that involvement in, or acquiescence to, such unlawful killings will never be tolerated"
Amnesty International statement
"Amnesty International continues to be gravely concerned at reports of an ongoing pattern of political killings of members of legal leftist organisations in various provinces nationwide," the statement said.
It urged the government to conduct prompt, thorough and impartial investigations of all the killings.
"In order to combat impunity, the authorities must also send a clear, unequivocal message to all members of the police, military and other security forces that involvement in, or acquiescence to, such unlawful killings will never be tolerated," it said.
The main leftwing party, Bayan Muna, says more than 80 of its members and officers have been assassinated over the past five years - including 32 last year.
The party has accused the military of instigating the killings and organising death squads, a charge repeatedly denied by military officials.
Arroyo imposed a state of
Bayan is led by Satur Ocampo, former spokesman of the underground Marxist umbrella, National Democratic Front.
Ocampo and four other legislators affiliated with his party have been holed up at the House of Representatives since 27 February, three days after Arroyo declared a state of emergency to thwart an alleged coup plot.
Arroyo lifted the emergency a week later.
The police have threatened to arrest them if they leave the congress compound.
Amnesty International said that in connection with the emergency decree, the "political left in particular may have been targeted for a repeated series of arrests on a variety of spurious charges".
Police have arrested Crispin Beltran of the Anakpawis party, a former labour leader, and charged him with rebellion.
The military has accused Bayan Muna and its allies of supporting the New People's Army, the armed wing of the Communist Party of the Philippines, which has been waging an insurgency for 36 years.
Amnesty International reminded the government that restrictions on freedom of expression and assembly during emergencies should be "strictly proportional to the dangers posed to the rights and freedoms of others".