The F-18 jet fighters landed at 8:20 a.m. and took off at 12:20 p.m., staying for only four hours.
US Embassy spokeswoman Karen Kelley said the stop was only for refueling after a flight from Japan.
The destination of the transport planes and jet fighters has to be kept secret, she added.
Each manned by a pilot and a weapons specialist, the six F-18s were filled up with some 20,000 gallons of aviation fuel immediately after they landed at Macapagal Airport.
The four hours of refueling gave the pilots and weapons specialists enough time to watch the World Series between the Arizona Diamondbacks and the New York Yankees on television at the Philippine Air Force terminal.
The C-130 transport planes arrived last Sunday, carrying 110 US Marine support personnel along with communications gear and other equipment.
President Arroyo was among the first world leaders to throw full support behind the US following the Sept. 11 terrorist attacks.
The US halted major exercises in the country and visits by US Navy ships in December 1996, when the government ended a legal guarantee that shielded American soldiers from prosecution for crimes committed here.
In May, 1999, the Senate approved a Visiting Forces Agreement, allowing the resumption of joint military exercises and visits by US troops.
US military advisers visited last week to assess the needs of the Armed Forces, which has been involved for months in a massive search for Abu Sayyaf terrorists holding about a dozen captives, including American missionary couple Martin and Gracia Burnham in Basilan. Ding Cervantes