Follow below steps to resolve this problem, when google shows malware code warning.
1. Login at the google Webmaster tool service login with your google account credentials:
2.Here go to Webmaster tools
3.Add your site for diagnose from the “Add a site” option there, it will provide you an meta code.
Place that code in the header of you index.php file of your site, this will ensure your ownership for the site.
3. Once your site ownership is verified by the google you can use the google diagnostic tools under your webmaster login panel to locate the malicious code on your site. It will let you know the location of malware code in your site.
4. Remove that code and perform the diagnose test again as in Step 3.
5.Click on the “Site Reconsideration” option in the left menu. Google will take around 24 hours to perform the test and reconsider your site again if malicious code is being removed correctly.
6. If malicious code is found and removed successfully with the above procedure google will reconsider your site and malware warning for the site will be removed by google.
Else if malicious code is not properly detected with the above steps, post your site details(site URL) and warning message details on the Webmaster forum by loging in there with your gmail account.
Webmaster Support Forum URL is: http://www.google.com/support/webmasters/
They will assist you in locating the malicious code on your server. Then follow the Step4 and Step5.