The service - which  started in May - provided Dundee with its only international air link.
Last month, the airline said it was temporarily rerouting the service, with passengers being taken by bus to Edinburgh Airport.
Flybe said the decision to suspend the flights was made because current radar coverage was not good enough.
The airline said it remained committed to exploring future opportunities from Dundee.
It said the route had proved "very popular" when it started in May.
A statement from the airline added: "However, due to the topography coupled with high levels of light aircraft activity in the surrounding area, it has become clear that enhanced radar coverage is required to accommodate the operation of our large passenger aircraft."
Simon Laffin, executive chairman of Flybe, said: "Serving Scotland is one of the most important parts of the Flybe business. We have tried very hard to find a way to operate out of Dundee, but we would need better radar coverage to operate in the area.
"We very much hope that this can be provided in the future to allow our flights to resume."
Flybe said it would continue to offer customers with existing bookings the option of a full refund, or a road transfer between Dundee and Edinburgh with a flight between Edinburgh and Amsterdam.
The airline Flybe is to suspend its Dundee to Amsterdam flights from next month.