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.

Former Grimsby boss Hurst was appointed on 24 October, with the Shropshire club at the bottom of the table.
After beating Oxford, losses to Sheffield United and Fleetwood plus a 0-0 draw at home to Port Vale have seen Hurst's side return to bottom spot.
"Sometimes you need a bit of a joker," he told BBC Radio Shropshire.
"I'm a believer you can have fun while working hard still. They're a quiet group. I don't know if they feel they're still getting to know me, but I want a bit more from them.
"Characters - that's what you sometimes need. I don't want them to feel down."
Shrewsbury host fellow third-tier side Fleetwood in the FA Cup second round on Saturday.

Alexander was centrally involved at McLaren for more than 40 years after being recruited by driver Bruce McLaren to help set up the team in 1963.
He left in 1983, two years after McLaren was taken over by current boss Ron Dennis, but returned in 1989 and worked there until he retired in 2008.
"Tyler was one of the first pillars of our company," said Dennis.
"Bruce couldn't have asked for a sturdier pair of shoulders upon which to help build the team's reputation. Quite simply, Tyler lived and breathed McLaren."
In the early years of the team, Alexander worked alongside Bruce McLaren and fellow American Teddy Mayer in F1, first as chief mechanic and then chief engineer before becoming a director of the company.
The company continued under Mayer following McLaren's death in a testing crash in 1970.
In the late 1960s, Alexander moved to run the company's successful programmes in the US, first in the CanAm sportscar championship and then in Indycar racing, before returning to F1 in 1979.
Dennis took over McLaren in 1981, first running it alongside Mayer before taking total control, and two years later Alexander sold his shares to Dennis and left the company.
He returned to the US to join Mayer in running an Indycar team, which recruited as engineer a young Adrian Newey, now Red Bull's chief technical officer and the most decorated design engineer in F1 with world titles at Williams, McLaren and Red Bull.
Alexander and Mayer were the joint team principals of the short-lived US-based F1 team Beatrice in 1985 and 1986. After its collapse, Alexander returned to Indycar racing before Dennis re-signed him as McLaren's special projects engineer in 1989.
During his final 20 years with the company, McLaren won six drivers' and five constructors' world titles with Ayrton Senna, Mika Hakkinen and Lewis Hamilton.
In a tribute to Alexander on the McLaren website, Dennis said: "Tyler was one of the finest of the old school: hardy, humble and wise, leaving a reputation and a legacy that will remain indelible in the history of international motorsport."
FlyBe's new daily Dundee to Amsterdam service has been rerouted "until further notice", the airline has confirmed.
[NEXT_CONCEPT]
Shrewsbury Town manager Paul Hurst has urged his squad to have more fun and lighten up, in a bid to help their League One relegation battle.
[NEXT_CONCEPT]
American Tyler Alexander, one of the key figures in the founding of the McLaren team, has died aged 75.