In order to convert the new v3 ppk file to pem, you need to use puttygen 0.75 or newer. At the time of writing this, v0.73 is the latest you can get using apt, but you can download and build the newest version of puttygen from source.
This answer on SuperUser explains how to do this for v0.76 for instance:
- If putty is installed, uninstall it
sudo apt remove putty-tools
- Download the unix source code of the 0.76 version of putty
mkdir putty_source_code
cd putty_source_code
wget https://the.earth.li/~sgtatham/putty/0.76/putty-0.76.tar.gz
- Extract the unix code
tar -xvf putty-0.76.tar.gz
cd putty-0.76
- Compile the unix code
./configure
make
sudo cp puttygen /usr/bin/
- Check if the version was installed correctly
puttygen --version # Should output something similar to `puttygen: Release 0.76`
- Remove the downloaded source code, you no longer need it now that you have installed it in /usr/bin
cd ../..
rm -rf putty_source_code
- Change to the directory with the .ppk file
cd <dir_with_ppk_key>
puttygen <ppk_key_name.ppk> -O private-openssh -o pem_generated_file.pem
You should now have the converted key on the directory
I had the same issue you were describing and using the steps above worked for me. I hope they will for you too.