Such problems were rare on the second-generation Emerald ferries despite the two incidents, Managing Director of Sydney Ferries Loretta Lynch told ABC radio on Tuesday.
A total of three steering issues had been recorded since Emerald ferries took to the harbour in July last year.
The Fairlight encountered difficulties while carrying passengers from Manly to Circular Quay shortly before 5pm on Monday.
The ferry master regained control of the vessel within seconds and decided to return to the wharf and drop off the passengers, Ms Lynch said.
"For precaution we took the vessel out of service."
That incident happened a day after the Clontarf suffered a steering failure.
"Both ... are being investigated very carefully," she said.
The Clontarf, Fairlight and Balmoral have all been removed from service and will be inspected by a maintenance team, a Transdev spokesperson told AAP.
Monday's incident led to two further services being cancelled before replacement ferries were launched.
"We had to remove that ferry while we're investigating the cause because safety is the most important thing for us," Ms Lynch said.
She rejected reports the Fairlight stalled in front of a large cruise ship.
Occasional disruptions to ferry, bus and train fleets were "par for the course" and assessments were being carried out as quickly as possible, NSW Premier Dominic Perrottet said on Tuesday.
"There are always mechanical challenges with fleets," the premier.
"My expectation is that those ferries are back on the water as quickly as possible, and that there is minimal disruption to that service," the premier said.
Labor Leader Chris Minns labelled the situation "a joke", telling AAP he believed the situation was caused by the government investing in foreign-built ferries.
"This is the second time one of these overseas built ferries has failed in as many days," he said.
"This is solely because (of Mr) Perrottet and the Liberals' obsession with buying overseas built ferries, trains and trams.
"It's cost thousands of jobs and billions of dollars and they can't even be used. What a joke."
Last month the government announced the return of the iconic Freshwater ferries for weekday operations, less than a year after the larger boats were removed from operations.
First launched in the 1980s, their recall came after the Emerald-class ferries were plagued with operational issues.
Cracks were found in hulls, windows shattered on the water and they struggled to operate safely in high swells or dock at very low tides.
