The NRMA-owned Manly Fast Ferry has confirmed it stood some deckhands down after they tested "non-negative" for illicit drugs on Monday, as revealed by the Herald's CBD column on Friday.

With fewer staff available, the NRMA said it had been forced to reduce the frequency of some of its tourist services that travel between stops including Taronga Zoo and Darling Harbour on Friday.

One of the then-new ferries in service in 2015. Ben Rushton

But a spokeswoman said Manly to Circular services were unaffected and it expects normal schedule times to operate across the weekend.

"Some deckhand staff returned non-negative results and others who did not make themselves available for the random drug test have been stood down indefinitely," a NRMA spokeswoman said.

"We’ve done this to give our passengers assurance around safety and that we have a zero tolerance policy around illicit drug use," the spokeswoman said.

The NRMA, which operates 11 fast ferry vessels through a subsidiary, is locked in a dispute with the Maritime Union over worker pay which has lasted for months.

About 80 fast ferry workers have gone on strike several times this year in a campaign for higher wages after an enterprise agreement was struck down in January.

The Fair Work Commission found the agreement did not pass the "better off overall test" that requires agreements to give workers a better deal than the fallback award.

No replacement deal has been signed since.

The Maritime Union wants wages closer to those paid by Transdev, the company that operates ferries for the NSW government, while the NRMA offered staff an immediate pay rise of 10 per cent, followed by annual rises of 2.5 per cent over three years.

An NRMA spokeswoman said the CFMMEU, of which the Maritime Union is a part, was notified when the staff were stood down.

But the spokeswoman declined to say how many ferry workers were stood down or what drugs were allegedly in their system because the company has not informed other workers. It is understood that will happen on Monday.

The Maritime Union declined to comment.