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the builtin PDF reader in the E6 and other symbian^3 phones uses QuickOffice, and currently this application does not support opening password-protected files.
I use Picsel smart office to view my PDF files and it works smoothly fast and does open password protected PDF's. You can find this application on Nokia Store.
search for "Smart Office" without the quotation marks of course. If it doesn't show up, then it is not available for your E6. I don't see why it shouldn't be though, as it is available for other symbian^3 devices.