How to Troubleshoot SSH Protocol Issues

Once a connection is successfully established, the SSH protocol negotiates an encrypted connection with the client based on establishing trust. Before you can even verify who you are on the system, the system attempts to establish an encryption method with your client. There are a few unique issues that can occur in this scope, and this tutorial covers how to identify them, how to resolve them, and additional resources to prevent them.

Before troubleshooting SSH issues, determine if migrating or redeploying is more appropriate for your situation, make sure the issue is truly with SSH, and review information and skills you need to troubleshoot successfully.


Host Key Verification Issues

When you connect to a server through an SSH client, the server attempts to identify itself using a host key. In situations where the host key changes, you may see a warning such as:

Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that a host key has just been changed.

In PuTTY, you get an equally ominous warning:


The server's host key does not match the one PuTTY has
cached in the registry. This means that either the
Server administrator has changed the host key, or you

Common causes for this issue include:

  • Rebuilding the Droplet from a snapshot or backup
  • Moving a Reserved IP to another Droplet
  • Reinstalling the SSH server through the package manager

To resolve this, you can clear your host keys.

Connection Closed or Reset By Peer

In some situations, connectivity is established at the socket level but disconnects during the host key verification phase.

OpenSSH clients may show this error:

Connection closed by port 22

PuTTY may show this error:

Server Unexpectedly closed network connection

Some common issues that may cause this error include:

  • The SSH service has crashed or is experiencing bugs.
  • The SSH service cannot initialize a connection due missing server host keys.

In a situation like this, a more thorough review of the protocol output is necessary. In most cases, you need to investigate this from the server through the Recovery Console. From there, make sure that the service is currently running and bound to the expected port.

Unable to Negotiate with Host

When initiating the SSH protocol, a shared secret is generated through a cipher negotiated between the client and the host.

An OpenSSH client may show an error like this:

Unable to negotiate with no matching key exchange method found.
Their offer: diffie-hellman-group1-sha1

PuTTY may show an error like this:

Couldn't agree a client-to-server cipher (available: aes128-ctr, aes192-ctr, aes256-ctr)

Some common issues that may cause this error include:

  • You have a modern OpenSSH client implementation and an older host that does not support a common cipher with the client.
  • You have customized your SSH client cipher list to only allow a selection that the server does not support.

To resolve this issue, you need to customize the supported ciphers in your SSH client.


Clearing Out Host Keys from Known Hosts

Host keys are typically stored in the ~/.ssh/known_hosts file on OpenSSH client implementations. PuTTY typically stores these in the Windows Registry (HKEY_CURRENT_USER\Software\SimonTatham\PuTTY\SshHostKeys).

In PuTTY, use the window that opens when you connect to select Yes to allow the connection and update the registry. Alternatively, you can manually remove the entry.

On an OpenSSH client, you can find the host entry in the ~/.ssh/known_hosts file and manually remove it. Another option is to use the ssh-keygen command:

ssh-keygen -R

This attempts to access and clear the matching host entry in the known_hosts file:

# Host found: line 2
/home/user/.ssh/known_hosts updated.
Original contents retained as /home/user/.ssh/known_hosts.old

You can then try to reconnect to your server normally.

Checking and Regenerating SSH Host Keys

If your SSH host doesn’t have its own private key to generate a shared secret, the connection is aborted. To check that the host has a private key, look in the /etc/ssh directory for a group of files named like sshd_host_*_key with corresponding .pub files.

If the files don’t exist, you need to regenerate them. You can do this using ssh-keygen as root or with sudo:

ssh-keygen -A

The output reports the actions taken, including a list of the keys generated:

ssh-keygen: generating new host keys: RSA DSA ECDSA ED25519

You can then try to reconnect to your server normally.

Customizing Supported SSH Ciphers

You can customize the supported SSH ciphers on your client machine when you need support for a deprecated cipher like SHA1. This is not a very common issue. It typically happens when you use a modern SSH client to connect to an old SSH server that hasn’t yet disabled weaker ciphers.

In OpenSSH, you can configure SHA1 using the KexAlgorithms option on the command line:

openssh -oKexAlgorithms=+diffie-hellman-group1-sha1 [email protected]

PuTTY should already include the Diffie-Hellman group 1 option in the Connection > SSH > Kex configuration.


If you need further help, you can open a support ticket. Make sure to include the following information:

  • The username, host, and port you are using to connect.
  • The authentication mechanism you expect to use.
  • The full output of the errors linked to the stage of error, including verbose output of the SSH client
  • All of the information you’ve gathered from troubleshooting so far.
  • Anything you were unclear about while referencing this article.

Including all the above diagnostic information and clarifying where you are encountering the issue when trying to connect can help us quickly get up to speed with where your need on the issue is.

Problems with SSH authentication includes permission denied with SSH keys and passwords.
Problems with SSH connectivity include hostname resolution errors and connections being refused or timing out.
Problems with SSH shell environments include being unable to fork a process, the system reporting it’s not a valid shell, or issues reaching the home directory.