Even, I had the same error.
From the Doc
When using the Command Prompt on Windows, the default configuration file name can cause a conflict with the truffle executable.If this is the case, we recommend using Windows PowerShell or Git BASH as these shells do not have this conflict. Alternatively, you can rename the configuration file to truffle-config.js to avoid this conflict.
I tried changing the config file first i.e. truffle.js to trufle-config.js, but then I got the same error of config file missing. But when I use it Windows PowerShell, it works like a charm.
Hope this helps