LinksAir, which previously ran the Welsh government-subsidised service, said it was out for tender but no contract had been signed with another airline.
But the Welsh government said alternative carrier, Citywing, had now stepped in.
Passengers were told to turn up and travel as normal on Monday.
A Welsh Government spokesman said: "The provider of the intra Wales service withdrew their service without notice today, but we have secured an alternative carrier to enable the service to continue without interruption."
The twice-daily return flights, running since 2007, get a Â£1.2m annual subsidy.
An assembly committee report warned in July 2014 that the north-south air link was underperforming.
AMs were told that in 2012-13, passenger numbers for the route were 8,406, down from 14,718 in 2008-09.
In June 2015, LinksAir reported a 40% increase in passenger numbers for the first six months of the year, compared to the same period in 2014.
However, in October, LinksAir had its safety licence revoked by the Civil Aviation Authority "to protect the travelling public".
Danish company North Flying took over the operation of the route on behalf of the company, which is based at Doncaster-Sheffield airport.
A new airline has agreed to take over twice-daily flights between Cardiff and Anglesey after they were suspended.