Dr Christine Wheatley's 11-month-old daughter Ellie has been denied full treatment because she is not blind as well as deaf.
Hampshire Primary Care Trust (PCT) has agreed to pay £33,000 for one cochlear implant but not an extra £18,000 for the second.
Dr Wheatley and husband Ed said the decision would leave Ellie at risk on roads and struggling at school.
Hampshire PCT said it made its decision after studying guidance from the National Institute for Clinical Excellence (Nice), which issues funding recommendations.
Nice currently only recommends 'bilateral' cochlear implants for deaf people under limited circumstances, such as where someone is also blind.
But some primary care trusts do fund bilateral implants for those who are simply profoundly deaf, said Dr Wheatley, 35, from Winchester, Hants.
She said: "We find it very frustrating knowing others families in identical situations have had their bilateral operations.
"Ellie has undergone nine months of assessments and the clinicians at the Cochlear Implant Centre in Southampton support bilateral implants for her.
"I believe the PCT only considered the extra cost of a second implant, not how much less her education will cost if she has both ears operated on now.
"We believe that morally Ellie should have the operation on the NHS."
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