Commentary for Numbers 1:49

אך את מטה לוי לא תפקד ONLY THOU SHALT NOT NUMBER THE TRIBE OF LEVI — The legion of the King is worthy to be numbered by itself (cf. Midrash Tanchuma, Bamidbar 15). — Another explanation is: The Holy One, blessed be He, foresaw that a decree would once be made against all those that had been numbered from twenty years and upwards, viz., that they should die in the wilderness (Numbers 14:29). He therefore said: Let these (the Levites) not be included amongst those now counted, in which case they must die, because they are Mine, since they did not sin by worshipping the golden calf (cf. Numbers Rabbah 3:7; Bava Batra 121b).

אך את מטה לוי, even though I had said “count all the heads of the community of Israel,” (verse 2) and it was understood that the Levites were included in this, they are distinct from the other tribes in that they will be counted separately, according to different criteria, such as —

לא תפקד…לא תשא. "do not count…nor take their sum, etc." The meaning is that the Levites should neither be counted by the traditional means of tendering a half shekel nor by any other means at the same time as the other tribes were being counted. Please refer to my comments in Parshat Ki Tissa on this subject.