The group, which was calling on Arroyo and her senior generals to step down over alleged corruption, later surrendered peacefully.
General Hermogenes Esperon Jr, the country's military chief, said the verdict showed that the judicial system "is taking its due course", adding that he appreciated the officers' guilty plea.
In welcoming Tuesday's ruling, Anthony Golez, the deputy presidential spokesman, said he hoped the men had "learned their lessons well".
"Those who committed crimes against the government and the Filipino people must pay the price for their anarchic actions," he said.
Last week all nine officers pleaded guilty after earlier denying the charge over the 2003 plot, prompting reports of a possible deal with the government.
Became Philippine president in 2001, replacing Joseph Estrada who was removed by popular revolt
Pledged reforms in government, more jobs, healthcare insurance and anti-terrorism to secure second term in 2004 elections
Now is faced with mounting public pressure to resign over alleged corruption and vote-rigging
Husband Jose Miguel and a former elections chief allegedly tried to gain kickbacks from Chinese telecom firm
Thwarted four coup and three opposition impeachment bids since taking power
Declared she will complete her term which ends in 2010
But prosecutors denied the government had struck any deal with the officers who are also facing separate court martial charges.
Richard Fadullon, the assistant state prosecutor, said they sought 20 years each for army captains Gerardo Gambala and Milo Maestrecampo, who were among four identified ringleaders, but were surprised with the decision.
"Judge Pimentel has his reasons and what the judge imposed was in accordance with the law," he said.
"It's harsher than what we expected."
Last year, one of the ringleaders, ex-navy lieutenant Antonio Trillanes, won a seat in the Philippine Senate while campaigning from behind bars.
The government said the 2003 mutiny was part of a larger plot to overthrow Arroyo, but the officers who led the action said they were protesting against alleged corruption and demanding the resignation of Arroyo and other officials.
In 2006, Arroyo crushed another coup plot and jailed at least two generals and several senior military officers who had withdrawn their support for her over allegations of corruption and vote-rigging.
Since taking power in 2001, Arroyo has survived four attempted coups and three opposition impeachments.