The error would happen if the file /var/cpanel/3rdparty/bin/php had a problem. To solve it, you can remove file /var/cpanel/usecpphp, and use the default PHP binary instead. After that, run the following command.

/usr/local/cpanel/scripts/makecpphp

Ref :

http://docs.cpanel.net/twiki/bin/view/AllDocumentation/WHMDocs/CpsrvdAndPhp