Fishermen found the 3.65-metre drone floating off Masbate island and dragged it to shore.
Provincial police chief Senior Superintendent Heriberto Olitoquit says they initially thought they had hauled in a bomb and alerted police.
"A technical evaluation determined that the object is one unmanned aerial vehicle," he said.
Superintendent Olitoquit said the drone had been turned over to the Philippines Navy.
Captain Rommel Galang, deputy commander of naval forces in the area, says the US embassy had been informed of the discovery and local authorities would eventually turn it over to them.
The US embassy in Manila released a statement on Monday saying it was looking into reports of the drone's recovery, without confirming the plane belonged to the United States.
"We are aware of reports that an apparently US-made unmanned aerial vehicle was recovered in the waters off of Masbate this weekend," the statement said.
"The recovered vehicle appears to be of the sort that is used as an air defence target in training exercises. This type of vehicle is not armed and not used for surveillance.
"We are trying to confirm this interpretation and to determine how and when it may have landed in the sea."
In an interview last year, President Benigno Aquino confirmed US drones were allowed to fly across the Philippines for reconnaissance purposes, but were not allowed to conduct strikes.
The Philippines is a close American ally and has long relied on its former colonial ruler for help in dealing with its many security threats.
The United States is also the Philippines' biggest supplier of military hardware.
About 600 US forces have been rotating in the southern Philippines since 2002 to help train local troops to deal with Islamic militants.
However, Masbate, where the drone was found, is many hundreds of kilometres from the Muslim insurgency-wracked southern regions and no US troops are known to operate there.
One major security problem in Masbate is the support there for communists who have been waging a decades-long rebellion that continues to claim dozens of lives every year.