"It is with profound sadness that we confirm that our Filipina (compatriot) was executed in China this morning," a sombre foreign department spokesman Raul Hernandez told a news conference.
"The Department of Foreign Affairs would like to express its deepest sympathy and condolences to the family of the Filipina as they mourn the loss of their loved one," he added.
"The life of every Filipino is valuable and we pray that this is the last time that a tragedy like this befalls any of our countrymen."
She was arrested along with her male cousin for heroin-smuggling in 2011 and both were later sentenced to death. But the cousin won a two-year reprieve, according to the Philippine government.
The woman was the fifth convicted drugs smuggler from the Philippines to be executed by China since March 2011, when two women and a man were put to death for the crime.
A second Filipino man was executed in December 2011.
All five executions were carried out despite intense lobbying by Philippine President Benigno Aquino to have the sentences commuted to life imprisonment.
The latest execution comes amid already rocky relations between the two countries, soured by overlapping territorial claims in the South China Sea.
Aquino spokeswoman Abigail Valte also extended the government's sympathies to the woman's family.
"However unfortunate, we hope that this will serve as a continuing lesson to our citizens not to allow themselves to be victimised and to fall prey to these (drug) syndicates," she said in a statement.
A total of 213 other Filipinos are in China jails on drugs offences, the foreign department said.
Some 28 of them -- apart from the woman executed today -- have already been sentenced to death but have been granted two-year reprieves, it said.
The mainly Catholic Philippines abolished the death penalty in 2006, and the 2011 executions of the four Filipino drug smugglers were met with widespread condemnation.