Passengers who have booked flights on the route are currently being taken by bus to Edinburgh Airport.
The airline said the decision was due to an "ongoing review" of its operation at Dundee Airport.
The service, Dundee Airport's first non-chartered international route, was launched in May.
It has been rerouted via Edinburgh since 10 November.
Dundee West MP Chris Law said at the time he was optimistic that rerouting the flights was a short-term issue.
A FlyBe spokeswoman said: "Due to the ongoing review of Flybe's operation at Dundee Airport, flights to Amsterdam Schiphol Airport will continue to operate via Edinburgh Airport until further notice.
"Passengers are being contacted and advised of the arrangements put in place to facilitate their transfer between the two airports.
"Flybe sincerely apologises to customers for any inconvenience resulting from this disruption.
"The airline remains committed to working with Dundee Airport to resolve this as quickly as possible."
The route is FlyBe's fourth under the UK government's Â£7m regional air connectivity fund.
The airline previously announced the service would begin operating on Saturdays from November due to popular demand.
FlyBe's new daily Dundee to Amsterdam service has been rerouted "until further notice", the airline has confirmed.