Could you post more information about your Apache configuration? Most likely, is is due to an AllowOverride None somewhere in your configuration. Try adding this:

<Directory "/var/www/wp-content/plugins/akismet/">
     AllowOverride All
</Directory>

That’s probably too permissive. You’ll want to limit it somewhat, but if this works then you know the root issue.

I ran into the same issue and fixed this by adding the following to my Apache conf:

<Directory /var/www/wp-content/plugins/akismet>
AllowOverride Limit
</Directory>

then reloaded Apache using “service apache2 reload”