I checked the file permissions on the master and they seems to look good:

[root@master user]# ls -l /etc/ipa/ca.crt
-rw-r--r--. 1 root root 1303 Apr  6 11:15 /etc/ipa/ca.crt

[root@master user]# ls -l  /var/lib/ipa/ra-agent*
-r--r-----. 1 root ipaapi 1708 Apr  6 11:14 /var/lib/ipa/ra-agent.key
-r--r-----. 1 root ipaapi 1241 Apr  6 11:14 /var/lib/ipa/ra-agent.pem

So, the problem is in something else.
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