You have it backwards. The other answer already lists the visa validity of three months, extendable by a further three months once for the residents of certain countries, including the UK.
What I am assuming you may be referring to is another requirement to be eligible: your passport must be valid when you intend to leave the country. Meaning, if your passport expires on the 1st June, you cannot enter Japan on 1st May and expect to stay a full three months, you will have to leave by the end of your passport validity.
Between the length of the landing permit and the passport validity, the shorter length counts.
Side note: unlike some other countries which require a passport valid for 3 or 6 months longer than the end of your visa period, Japan accepts passports with a shorter validity. That might be what the site you were looking at was emphasising.