Short answer. No. Article 91 provides that the term of prescription does not run while the offender is absent from the country. Time spent abroad is simply not counted, so a long absence does not let an offence quietly lapse — though the dates of departure and return still have to be established.
What the law says
The term of prescription shall not run when the offender is absent from the Philippine Archipelago.
Revised Penal Code, Article 91 — When Prescription Starts Running. Read the full provision →
Absence takes the time out of the count
The last sentence of Article 91 is short and absolute: the term of prescription shall not run when the offender is absent from the Philippine Archipelago. The effect is arithmetical. Days the offender spends outside the country are not counted towards the period at all, so a person who leaves does not run down the clock by staying away. The rule exists because prescription assumes the offender was available to be proceeded against; where he was beyond reach, the Code declines to treat the passing time as if it had been an opportunity to prosecute.
The reason for the absence is not in the text
The article draws no distinction between someone who fled and someone who was simply working, studying or living abroad. It speaks only of absence. That matters to both sides of a case: a complainant does not have to prove flight to get the benefit of the rule, and a person who left for entirely ordinary reasons does not escape it by showing his motives were innocent. What the rule does not do is create liability — it affects only the computation of time, and every other question in the case is unaffected.
The clock resumes on return
Suspension is not extinction. Once the offender is back in the country the term picks up where it stopped, carrying forward whatever had already run before he left. So the practical figure is the total period less the days actually spent here, and a case can still prescribe despite a long absence if enough countable time has passed. Where there have been several trips, the computation is a matter of adding the resident intervals, which is why the arrival and departure dates matter individually rather than in the aggregate.
Proving the absence
The rule is easy to state and harder to document, because the record that establishes it usually belongs to the government rather than to the complainant. Travel records, entries in a passport, employment contracts abroad and remittance histories are the sorts of material that fix the dates. A complainant who suspects an offence has been sitting dormant should raise the absence at the outset rather than after a prescription objection is made, and should take whatever timeline he can assemble to a lawyer while the documents are still obtainable.