He said William McNeilly's allegations were either factually incorrect or the result of misunderstanding or partial understanding.
The Royal Navy submariner has claimed missile programme system on the Clyde was a "disaster waiting to happen".
He wrote a report, detailing "serious security and safety breaches".
In a statement addressing the 25-year-old's concerns, Mr Fallon insisted that neither the "operational effectiveness" of the fleet "nor the safety of our submariners or public have been compromised".
The UK's Defence Secretary Michael Fallon has said a whistleblower's concerns about Trident nuclear submarine safety have not been proved.