You don't say what phone you have or what dialer app you are using. Have you tried going into the dialer's settings and enabling/disabling the call waiting notification? It is a setting that interacts with your carrier's service, so if that does not work you should call your carrier about the issue.
On my phone:
open dialer
menu
settings
call
more settings
(wait for the phone to read the settings from the network)
call waiting
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