I checked my command issued with the nagios account, and noticed that i forgot to change the $HOSTADDRESS$ variable to the real name of the backupexec server. I ran the command with the correct hostaddress and noticed it now returns the status of the backupexec service.
/usr/local/nagios/libexec/check_nt -H servername -p 12489 -v SERVICESTATE -d SHOWALL -l BackupExecAgentBrowser
So afterall it got nothing to do with priviledged. My apologies for any inconvenience caused.
Eventually the problem is solved. All credits go to my colleague who found that check_nt seams to be outdated by check_nrpe.
To make things work do the following:
-on the particular windows servers open the NSC.ini
file, uncomment allow_arguments
and change its value from 0
-use this code in the cfg file for the windows server
command_line $USER1$/check_nrpe -H servername -c CheckServiceState -a ShowAll BackupExecAgentBrowser