What are the connotations of the words "al-Pi Hashem"?
Rashi: When Moshe asked Hashem how he could possibly enter the Levi'im's tents 1 to find out how many children they had, Hakadosh-Baruch-Hu replied 'You do what you have to do, and leave the rest to Me! Moshe then went and stood outside the Levi's tents, whilst the Shechinah went in and let him know via a Bas Kol how many children there were in each tent. Therefore the Torah writes "By the mouth of Hashem".
Since, as opposed to the counting of the other tribes, Moshe was told to go and count them - and not for the people to come to him.