Dumbledore is not affiliated with or a representative of the Ministry of Magic.
At the time that Voldemort went to Dumbledore seeking a position as DADA teacher, he had a reputation, mostly terrible rumors without any substance, but not enough in the wizarding world to try him for or hold him for anything.
It was only after this, when he began to actively attacking the wizarding world, that a true 'war' began.
And let's not forget that if the head of the Ministry of Magic was anything like Fudge, he'd be incredibly reluctant to take any unilateral action against a single man, for fear it would reflect very poorly on him.
And because they were only rumors, rumors that Dumbledore largely knew to be true but rumors to the Ministry, they had no reason to be seeking out and dogging down a man who, although a bit suspicious, was not guilty of anything, yet.