Dozens of beatings, rapes and electrocutions are being recorded by the country's human rights commission every year, with many other cases going unreported, Amnesty secretary general Salil Shetty told reporters.
"Torture by the police is very widespread and routine," Shetty said.
Shetty said ending torture could be a "very important legacy" for Aquino, whose six-year term will end in 2016, but he accused the president of not doing enough to reform the police force.
"If you don't acknowledge the problem, there can be no solution," Shetty said.
Quoting data from the Philippine human rights commission, Amnesty said 457 torture cases were reported from 2001 to the middle of this year. The 75 cases recorded in 2013 was the highest in a single year.
But five years after the Philippines passed a landmark anti-torture legislation under previous president Gloria Arroyo, there have been no convictions, Shetty said.
"The single, most important reason why there is torture in the Philippines is they (police) get away with it," he said.
He said low salaries also contributed to the problem, with police officers torturing to extract confessions or extort money.
Amnesty also recommended establishing a body that is independent from the police to handle reports of torture, as the current system sees police investigating themselves.