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This question already has an answer here:

Since we noticed that some user on our internal network use FTP client like FileZilla or WinSCP that store password as plain text, we wonder, is there any FTP client (windows) that store passwords in a "secure" way?

Edit

Also, we know that could use cerificate and SSH methods, but question is only about password storage.

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marked as duplicate by fixer1234, DavidPostill, surfasb, Mokubai Jan 29 '15 at 22:24

This question was marked as an exact duplicate of an existing question.

For SCP/SFTP method there is Bitvise Tunnelier that encrypt the password on the profile

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Total Commander

It does not store password as FileZilla does but is considered to be more "secure".

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And that was our first idea ..... – DonCallisto Jan 17 '13 at 16:12
    
@DonCallisto You can read more about it in this blog post – Ofiris Jan 17 '13 at 16:13

WinSCP does not save passwords in plain text.

Though obviously it can only "obfuscate" the password. It is not possible to securely encrypt passwords in a way that still allows for automatic use.
See http://winscp.net/eng/docs/security_credentials

For better security, you can enable password encryption using master password:
See http://winscp.net/eng/docs/master_password

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