You *must* have to check your *entire* server, with a clean boot.
If you don't have phisical access to the server, you must ask to it who have.
After that, try to install Maldet, with script:
/scripts/install_maldet
Check if you have some antivirus installed too.
Normally, if you have some malware in your server, discovered by accessing some page, you must check that page individually, and restore the original page or program.