Short answer. Not from the date of the crime, but from the day it is discovered by the offended party, the authorities or their agents. Filing the complaint or information interrupts the period, and it does not run at all while the offender is absent from the Philippines.
What the law says
The period of prescription shall commence to run from the day on which the crime is discovered by the offended party, the authorities or their agents
Revised Penal Code, Article 91 — When Prescription Starts Running. Read the full provision →
Discovery, not commission
This distinction saves cases that would otherwise be dead on arrival. Where a crime was concealed — falsified documents, misappropriated funds, a forged signature on a title — the clock does not begin on the day the offender acted, but on the day the offence was discovered by the offended party, the authorities or their agents. Discovery by any of those three starts it, so a victim who learns of the crime years later is not automatically barred. What counts as discovery is a question of fact, and courts look at when the complainant actually knew, or was in a position to know, that a crime had been committed against him.
Interruption by filing
The running period is interrupted by the filing of the complaint or information. That is why the practical advice is always the same: file, and file early. Once a proceeding is under way, the clock stops. It starts running again only when the proceedings terminate without the accused being convicted or acquitted, or where they are unjustifiably stopped for any reason not imputable to him. So a case dismissed on a technicality, or shelved for reasons the accused did not cause, revives the period rather than closing the matter permanently — but the time already consumed before filing is not given back.
Absence from the country freezes the clock
The article closes with a rule aimed squarely at offenders who leave: the term of prescription shall not run when the offender is absent from the Philippine Archipelago. A person who commits a crime and flies out cannot simply wait abroad for the period to lapse. For a complainant, this means an offender's departure is not the end of the road, though proving the dates of absence usually requires travel records obtained through the proper channels. It is one of the reasons a complaint is worth filing even when the respondent is believed to be overseas.
What this article does not tell you
Article 91 explains only how the period is computed. It does not say how long the period is — that depends on the penalty attached to the particular felony, and the ranges run from a couple of months for the lightest offences to twenty years for the gravest. Crimes under special laws are governed by their own prescription statute, not by this article, and the rules for offences punished by ordinances differ again. Prescription is also a defence the accused normally raises, and getting the computation wrong in either direction is costly. If you are weighing whether a complaint is still viable, have counsel work out the applicable period against the actual dates before you conclude that it is too late.