Sorry, this is not actually WinSCP question, but generic Linux/Ubuntu question.
Please ask at https://superuser.com/ or https://askubuntu.com/ or at AWS support.

I have setup an Amazon AWS EC2 instance running Ubuntu.

Now, I am trying to connect it with the WinSCP.

Connection part is completed using the public key and I can browse files as well as use PuTTY to perform commands. By default an user named ubuntu is created. Problem starts when I try to perform file transferring.

If, I just drag and drop files from my computer (WinSCP left side) to the remote machine (WinSCP right side) it shows an error,

Permission denied.
Error code: 3
Error message from server: Permission denied

Now, there are certain resolutions available over the net to handle that,
https://stackoverflow.com/questions/28261503/get-permission-to-work-with-files-on-my-amazon-ec2-ubuntu-server-using-ftp-winsc

In a jest, I have to provide permissions to the concerned folders.

Here the problem starts, the moment I execute sudo chown.. command, it shows me a different error,

sudo: /etc/sudoers is owned by uid 1000, should be 0
sudo: no valid sudoers sources found, quitting
sudo: unable to initialize policy plugin

This leads to the following resolution,
https://askubuntu.com/questions/513523/sudo-doesnt-work-etc-sudoers-is-owned-by-uid-1000-should-be-0

Now, it asks me for the password,

==== AUTHENTICATING FOR org.freedesktop.policykit.exec ===
Authentication is needed to run `/bin/chown' as the super user
Authenticating as: Ubuntu (ubuntu)
Password:

Probably, I am going too far and it is not the way to resolve the matter. Regarding the password, I have a public key file so, can't enter one when prompted. Can any one have any idea regarding the problem and solution ? If I try to make the current user a super user that too require root permission.