Last month's snub against multi-award-winning actress Nora Aunor sparked a nationwide furore with millions of fans insisting no one deserved a "national artist" prize more than the 61-year-old fondly nicknamed the "Superstar."
"Ms. Nora Aunor has been convicted for drugs and was punished for it.... By making her a national artist are we putting out the right message?" Aquino told a news conference aired on national television.
"I respect her and I recognise her body of work. But our message of zero tolerance against drugs takes priority."
The Order of National Artist award, issued by presidential proclamation, recognises a person's significant contributions to the development of Philippine arts and letters.
The honour includes a cash prize, monthly pension for life and a state funeral when the awardee dies.
Reacting to the snub, Aunor on Sunday said she was hurt by Aquino's action but overwhelmed by the public support.
"The Filipino masses ... have conferred the highest honour on me, by declaring me the people's national artist in their hearts," she said.
Six awardees were announced last month, taking the total to just 66, including six in the film industry, since it was created in 1972.
From humble beginnings Aunor -- born Nora Villamayor -- burst onto the entertainment scene in the 1960s as a singer with a powerful, soulful voice.
She also starred in movies where her petite, dusky looks broke stereotypes of fair-skinned leading ladies patterned after Hollywood.
Aunor has won several "Best Actress" awards at local and international film festivals.
Last year she took home the "Best Actress" trophy at the annual Asian Film Awards in Hong Kong for her powerful portrayal of a midwife in the locally produced "Thy Womb".
But her personal life has suffered several setbacks including an arrest in the United States for illegal drug possession, and ties to various scandal-plagued Filipino politicians.
In 1972 she campaigned for Ferdinand Marcos who later ruled as a dictator, and she also endorsed the presidential candidacies of fellow movie star Joseph Estrada in 1998 and Gloria Arroyo in 2004.
Current president Aquino has been at odds with all three.