There are three types of encryption you can enable for your data on transit:
1- Munki client <--> Munki server encryption. This is explained in the Munki wiki
2- MR-php web view (when you visit the website to see the data). This is accomplished in different ways depending on wether you use Apache, nginx...
3- MR-php client (scripts) <--> MR-php server. This is accomplished by doing the curl with the https. This also needs Apache, nginx or else to be properly configured with ssl/tls
An optional fourth item to limit non-legit MR-php clients from sending data to your MR-php server is accomplished by using a passphrase. Data in transit is sensitive to eavesdropping. Therefore is not an encryption but instead a simple filter.
I think you are looking for #3. Here a simple example of how to accomplish that:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 8987 0 8987 0 0 17517 0 --:--:-- --:--:-- --:--:-- 17518
Retrieving munkireport scripts
Configuring munkireport
+ Installing ard
+ Installing bluetooth
...
bash-3.2$ defaults read /Library/Preferences/MunkiReport.plist BaseUrl
bash-3.2$ sudo /usr/local/munki/managedsoftwareupdate -vvv
Password:
Managed Software Update Tool
Copyright 2010-2014 The Munki Project
Starting...
Performing preflight tasks...
preflight stdout: Munkireport: # Executing scripts in preflight_abort.d
Munkireport: # Executing scripts in preflight.d
Munkireport: Running bluetooth.sh
Munkireport: Running directoryservice.sh
Munkireport: Running disk_info
...
_
Noel