Found out, that ssh will relay that error if identity that shall be used is a 
link to actual file.
I have generated RSA keys using OpenSSL and stored them into 
~/.ssh/id_rsa.pub.pem and ~/.ssh/id_rsa.key.pem
Then I converted ~/.ssh/id_rsa.pub.pem into OpenSSH format using ssh-keygen
Then I created a link: ln ~/.ssh/id_rsa.key.pem ~/.ssh/id_rsa
Then I edited /etc/ssh/ssh_config such that there was only one line 
IdentityFile ~/.ssh/id_rsa
Then I tried to log into remote machine - the result was: sign_and_send_pubkey: 
signing failed: agent refused operation

Maybe I am missing something and there is a configuration option that
follows links?

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https://bugs.launchpad.net/bugs/1569019

Title:
  rsa ssh login fails with "sign_and_send_pubkey: signing failed: agent
  refused operation" error

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