Spokesperson Harry Roque made the comment at the election commission and told reporters that Duterte had decided he would run in the elections. Roque did not say which position the president will file his candidacy for.
Duterte is not eligible to run for president again.
Monday's deadline for Philippine political parties to finalise candidates for next year's election is keeping voters on the edge, with last-minute changes expected in unpredictable but significant presidential and vice-presidential races.
Roque's remarks run counter to those on Saturday by Duterte's communications chief, who said the president would register to run for vice president, and challenge his daughter, Sara Duterte-Carpio, who is vying for the same position.
In the Philippines, the president and vice president are elected in separate contests.
Duterte can run for other posts, such as senator, congressman, mayor or governor. He was mayor of Davao City before running for president in 2016.
His 43-year-old daughter had been expected to run to succeed him as president due to her popularity and clear lead in all opinion polls this year on preferred candidates.
She however signed on to run for the vice president's post, but can still change her mind.
It was not yet clear who Duterte-Carpio will run with, but presidential aspirant and son of late strongman, Ferdinand Marcos Jr. has said he wants her to be his running mate.
Candidates have until 0900 GMT on Monday to withdraw or switch positions by way of substitution.