Short answer. Yes. The law expressly gives a father the right to go to the regular courts to prove non-filiation — that he is not the child's father — during his lifetime. This matters most where a child has been using his surname, because recognition of paternity is what allowed that surname to be used in the first place.
What the law says
the father has the right to institute an action before the regular courts to prove non-filiation during his lifetime
RA 9255, Section 1 — Surname Of Illegitimate Children. Read the full provision →
The father's right to prove non-filiation
The answer is written into the law amended by RA 9255. It provides that "the father has the right to institute an action before the regular courts to prove non-filiation during his lifetime." So a man who is being treated as a child's father — whose surname the child carries — is not left without a remedy. He can bring an action in the regular courts and put the question of paternity to proof. The right exists precisely because recognition can be asserted on the strength of documents, and the law gives the man named as father a way to contest that he is the father at all.
"During his lifetime" is a real limit
The phrase is not decoration. The right to prove non-filiation is personal to the father and must be exercised while he is alive. It is his action to bring, and the window is his lifetime — it is not a claim his relatives or heirs can take up and litigate after he has died. A father who suspects he is not the child's father therefore cannot simply leave the matter unresolved indefinitely, expecting others to sort it out later. If he wishes to contest filiation, the law contemplates that he does so himself, in his own lifetime.
Why this is tied to the surname
By default, an illegitimate child uses the mother's surname and is under her parental authority. The child may use the father's surname only where filiation has been expressly recognised — through the record of birth in the civil register, or by an admission in a public document or a private handwritten instrument made by the father. That recognition is the hinge. Where a father says the recognition was mistaken, procured, or simply untrue, the action to prove non-filiation is the route to challenge the very basis on which the child came to bear his surname.
What the action decides, and what it does not
This is a matter to be proved in court, not settled by a bare denial. The father who brings the action must establish non-filiation on evidence, and the court decides on that evidence — so the outcome turns on what can be shown, not on the strength of the father's belief. Filiation carries real consequences beyond a name, including support and successional rights, which is why the law channels the dispute into a proper judicial proceeding rather than leaving it to private assertion. This is general information about the right the statute grants, not advice on a particular case.