Stone was responding to calls from the Canadian Taxpayers' Federation to end the free rides, after recent announcements of financial stress, service cuts, and a reduction in seniors' discounts from the company.
The minister told the CBC that scrapping the seniors' discount was the hardest decision he had ever had to make in his career, but said that he was speaking to BC Ferries about ending the free rides.
"If making changes to their employees passes can get them to their $54 million target, then that's a decision BC Ferries can certainly make," said Stone.
BC Ferries still has not revealed exactly how many free passes have been issued and say their antiquated computer system is still working on the data.
Claire Travena, NDP Transportation Critic, is troubled by the lack of information.
"BC Ferries can't come up with a single figure," said Travena.
"We know that they've been upgrading their computer system ... You can track down your own ferry rides, why can't they track down how many people are actually using this?"
BC Ferries has revealed that back in 2010, some 4200 staff, 3200 family members and some contractors had the free passes, which also cover vehicles.
CBC News has calculated that, if all 7400 passholders rode the ferry once a month, at the average fare reported to the Ferry Commission of $105 per trip, free pass use represents more than $9 million per year in lost revenue.
By comparison, that figure is $3 million more than the provincial savings of approximately $6 million per year from cutting seniors' discounts.
BC Ferries president Michael Corrigan says it has no plans to touch staff passes, which are a taxable benefit and, he says, cost nothing.
"Because we sail at 50 percent capacity, there is really no cost to BC Ferries."
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