Bamidbar 1:2 

וידבר… במדבר סיני … באחד לחדש וגו׳ AND [THE LORD] SPOKE [UNTO MOSES] IN THE DESERT OF SINAI … ON THE FIRST DAY OF THE [SECOND] MONTH … [TAKE YE THE SUM OF ALL THE CONGREGATION] etc. — Because they were dear to him, He counts them every now and then: when they went forth from Egypt He counted them (Exodus 12:37), when many of them fell in consequence of their having worshipped the golden calf He counted them to ascertain the number of those left (cf. Rashi Exodus 30:16); when he was about to make His Shechinah dwell amongst them (i. e. when He commanded them to make a Tabernacle), He again took their census; for on the first day of Nisan the Tabernacle was erected (Exodus 40:2) and shortly afterwards, on the first day of Iyar, He counted them.

וידבר. במדבר סיני באחד לחדש וגו'. מִתּוֹךְ חִבָּתָן לְפָנָיו מוֹנֶה אוֹתָם כָּל שָׁעָה — כְּשֶׁיָּצְאוּ מִמִּצְרַיִם מְנָאָן, וּכְשֶׁנָּפְלוּ בָּעֵגֶל מְנָאָן לֵידַע מִנְיַן הַנּוֹתָרִים, כְּשֶׁבָּא לְהַשְׁרוֹת שְׁכִינָתוֹ עֲלֵיהֶם מְנָאָם, בְּאֶחָד בְּנִיסָן הוּקַם הַמִּשְׁכָּן וּבְאֶחָד בְּאִיָּר מְנָאָם:

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 לא תפקד. כְּדַאי הוּא לִגְיוֹן שֶׁל מֶלֶךְ לִהְיוֹת נִמְנֶה לְבַדּוֹ (תנחומא); דָּ"אַ, צָפָה הַקָּבָּ"ה שֶׁעֲתִידָה לַעֲמֹד גְּזֵרָה עַל כָּל הַנִּמְנִין מִבֶּן עֶשְֹרִים שָׁנָה וָמַעְלָה שֶׁיָּמוּתוּ בַמִּדְבָּר, אָמַר אַל יִהְיוּ אֵלּוּ בִכְלָל, לְפִי שֶׁהֵם שֶׁלִּי, שֶׁלֹּא טָעוּ בָעֵגֶל (שם; בבא בתרא קכ"א):

1:51 

והזר הקרב AND THE LAYMAN THAT COMETH NIGH to this service of theirs,

והזר הקרב. לַעֲבוֹדָתָם זוֹ:

3:16

על פי ה'. אָמַר מֹשֶׁה לִפְנֵי הַקָּבָּ"ה, הֵיאַךְ אֲנִי נִכְנָס לְתוֹךְ אָהֳלֵיהֶם לָדַעַת מִנְיַן יוֹנְקֵיהֶם? אָמַר לוֹ הַקָּבָּ"ה, עֲשֵׂה אַתָּה שֶׁלְּךְ וַאֲנִי אֶעֱשֶׂה שֶׁלִּי, הָלַךְ מֹשֶׁה וְעָמַד עַל פֶּתַח הָאֹהֶל וְהַשְּׁכִינָה מַקְדֶּמֶת לְפָנָיו, וּבַת קוֹל יוֹצְאָה מִן הָאֹהֶל וְאוֹמֶרֶת כָּךְ וָכָךְ תִּינוֹקוֹת יֵשׁ בְּאֹהֶל זֶה, לְכָךְ נֶאֱמַר עַל פִּי ה':

על פי ה׳ [AND MOSES NUMBERED THEM] ACCORDING TO THE WORD OF THE LORD — Moses said to the Holy One, blessed be He, “How can I enter their tents to ascertain the number of their babes?!” Thereupon the Holy One, blessed be He, replied to him, “You do your share and I will do Mine!’ Moses accordingly went and stationed himself at the entrance of each tent, the Shechinah having gone there beforehand, and a divine voice issued from the tent, saying, “So-and-so many babes are in this tent”. It is on this account that it states, “[and Moses numbered them] according to the word (by the mouth) of the Lord” (Numbers Rabbah 3 9).