Check for the file

http://horsetransport.ru/CMS/yandex_648b3726073286c3.php

Do a scan of your PC and make sure there are no Trojans/viruses capturing your ids/passwords, change ALL passwords especiallly FTP, it is likely your passwords have been compromised. Never store/save your passwords in your FTP client, use secure FTP if available.

Once the site is secure and clean you need to submit a request for review in you Google WMT account to have the warning removed. If you have not verified ownership of the site you will have to do so first. The following reference explains the procedure.

http://sites.google.com/site/webmasterhelpforum/en/faq-malware-and-hacked-sites