Commentary for Makkot 2:4
לְהֵיכָן גּוֹלִין, לְעָרֵי מִקְלָט. לַשָּׁלשׁ שֶׁבְּעֵבֶר הַיַּרְדֵּן וְלַשָּׁלשׁ שֶׁבְּאֶרֶץ כְּנַעַן, שֶׁנֶּאֱמַר (במדבר לה) אֵת שְׁלשׁ הֶעָרִים תִּתְּנוּ מֵעֵבֶר לַיַּרְדֵּן וְאֵת שְׁלשׁ הֶעָרִים תִּתְּנוּ בְּאֶרֶץ כְּנָעַן וְגוֹ'. עַד שֶׁלֹּא נִבְחֲרוּ שָׁלשׁ שֶׁבְּאֶרֶץ יִשְׂרָאֵל, לֹא הָיוּ שָׁלשׁ שֶׁבְּעֵבֶר הַיַּרְדֵּן קוֹלְטוֹת, שֶׁנֶּאֱמַר (שם) שֵׁשׁ עָרֵי מִקְלָט תִּהְיֶינָה, עַד שֶׁיִּהְיוּ שֶׁשְׁתָּן קוֹלְטוֹת כְּאֶחָד:
Whither is one exiled to the cities of refuge? To the three across the Jordan and the three in the land of Canaan, as it is written (Numbers 35:14): "The three cities shall you provide across the Jordan; and the three cities shall you provide in the land of Canaan." And as long as the three in Eretz Yisrael had not been designated, the three across the Jordan did not grant refuge, it being written (Ibid. 13): "Six cities of refuge shall there be" — they must all be capable of granting refuge as one. [And forty-two cities of the Levites also all granted refuge. It is just that these six cities granted refuge whether or not the slayer entered there with the intent that they do so, whereas the forty-two cities granted refuge only where there was intent, but not otherwise; and if the blood-redeemer killed him there (in the absence of such intent), he is not liable.]
Bartenura on Mishnah Makkot
English Explanation of Mishnah Makkot
Not until three cities were selected in the land of Israel did the [first] three cities beyond the jordan receive fugitives, as it says, “Six cities of refuge in all” (Numbers 35:13), until all six could simultaneously receive fugitives.
Mishnah four begins to discuss the refuge cities, those cities to where the accidental killer would flee.
This mishnah begins to discuss the cities of refuge to where the accidental killer would flee in order to protect himself from the blood avenger. There were three cities on one side of the Jordan river (where the country of Jordan currently exists) and three in the land of Israel. Although the land on the other side of the Jordan river was conquered first and assumedly its refuge cities were assigned before the remainder of the land was conquered, nevertheless these refuge cities were not functional until all six had been conquered and assigned.