Maybe he wasn't. If the accusation is false, the accuser(s) need not have had private time with him.
The headline is misleading: if the investigation is being conducted by priests from outside the diocese, and not affiliated with SOLT, that isn't really "internal." Presumably the writer meant an investigation by the church, rather than by the police, but since fornication isn't a crime, there's no possible police involvement.
That was my thought, too. This isn't like the priests accused of abuse of a minor, so the secular authorities wouldn't necessarily need to be be involved.