The gesture affects about $15 million dollars that have been withheld over the last five years, a fraction of Washington's total military assistance to the South East Asian island.
Albert del Rosario told reporters that the aid restriction had been lifted "sometime last year," but did not explain why it had been lifted.
A day earlier, US Assistant Defense Secretary David Shear said that Washington had provided $300 million in military-related assistance since 2001 and would provide another $40 million in 2015 as part of America's support to modernize the poorly-equipped Philippine military, which is one of the weakest in the region.
Philippine-US defense relations have been complicated by leftist and nationalist groups who oppose the longstanding alliance and who have protested against any US military presence or assistance to the Southeast Asian nation.
Previously, human rights groups have successfully lobbied US legislators to cut military aid over the Philippine military's alleged failure to improve its human rights record.
Human rights groups have accused Philippine security agencies of committing abuses in its counter-insurgency program against both communist and Muslim extremist insurgencies.
The Philippines and the United States signed an agreement in April to allow a bigger US military presence on Filipino territory, a deal which would see more US troops rotate through the Philippines for joint military training exercises.
Philippine Navy Seals aboard the Rigid Inflatable boat during Take-Down Ship demonstration.