Staffing issues caused a total of 85 missing sailings since mid-June.
But things are improving, said David Moseley at a community meeting on Tuesday night.
"Fifteens straight days now -- not that I'm counting -- that we haven't missed sailings," he said.
But now a new Coast Guard review mandates more staff on some boats -- a move that will cost about $3 million over the next 14 months, according to the state.
"That's additional money that we don't have," said Moseley.
In addition to the cost, Secretary of Transportation Paula Hammond, in a letter to the Coast Guard, said it is not possible to implement the additional licensed mate position within the 30-day time frame. She asked for a delay in implementing that part of the mandate.
But the International Organization of Masters, Mates and Pilots, a union that represents licensed mates, says it is possible.
The Problem Solvers obtained a copy of the letter the union sent to Hammond which states that the union has ample qualified personnel and that Hammond "does not accurately describe the ability of the (union) to provide Deck Officers."
Whenever that additional staffing is added, it will cost the state to do it.
"Working with the governor's office and Legislature, we'll have to figure that out in the end," said Moseley.
And looking to the next budget cycle, one proposal would cut late night and some other runs to save the system close to $5 million.
"Well, it is the reality. I'm very aware of that," said Joan Dingfield of the Bremerton Ferry Advisory Committee. "I've followed along through the whole ferry funding study that went on in 2008 and 2009, and there is no money."
Whether late-night and other runs are eliminated is entirely up to lawmakers. And when the legislative session starts, there will be new people in key positions following last week's election.