Linux permission change on Reboot

Everytime the linux server is rebooted, permissions are changed on var/run directory causing issues with a daemon. Is there anyway to set the permissions so they do not change?

Welcome!

/var/run/ is in memory, and recreated at system boot.

Do you have systemd? If yes, then I suggest systemd-tmpfiles to create the desired (sub-)directory with the permissions at boot.
Consult the manual page

man tmpfiles.d
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