As the waterside portion of the massive, multi-million-dollar Woods Hole terminal reconstruction project comes to an end, Steamship Authority governors reluctantly approved more than $1.3 million in change orders at their meeting Tuesday.

Governors spent more than an hour discussing and dissecting two change order requests from contractor Jay Cashman Inc., both involving the recent underwater discovery of rocks and boulders that are obstructing the installation of dock pilings.

The two change orders bring the cost of the marine part of the project to more than $52 million — about 20 per cent higher than the original bid price of $43 million, including roughly $9 million in change orders.

The land side portion of the project, which includes a new ticket office in Woods Hole, has not begun. Recent cost estimates are in the range of $30 million.

But with change orders a consistent theme throughout the past four years of marine work, SSA governors on Tuesday wasted no time in expressing their exasperation.

“It’s no secret how horrible I think these change orders are,” New Bedford governor Moira Tierney said. “I don’t know that the process is really providing us the level of scrutiny that we should have, on this contract, with the huge cost overruns.”

“It’s constant . . . I believe we have a fiduciary responsibility to provide a level of scrutiny to what’s going on here that we are not doing right now,” she added.

“When does it stop?” Vineyard governor Jim Malkin asked.

“It doesn’t,” Ms. Tierney replied.

Ms. Tierney requested an informal audit of the process, and Falmouth governor Kathryn Wilson asked whether it was worth not paying the change order, which would cause a work stoppage. But SSA senior managers said it was critical to complete the work before summer, when the third ferry slip will be needed.

Dino Fiscaletti, a consultant on the project, said the underwater issues causing the change orders arose from the challenging Woods Hole seafloor topography.

“These are the kinds of situations the Steamship Authority has been dealing with for the past four years,” Mr. Fiscaletti said. “There’s two large holes we scoured out, one was filled with rocks, one was filled with sand. And we’ve got a head dolphin over the one filled with rocks.”

Frustrated governors approved the two change orders 4-1 and 3-2, with Ms. Tierney dissenting in both votes and Ms. Wilson dissenting in the second one. But all agreed that the nature of the bid process, which allowed for a built-in contingency fund, left them feeling boxed in.

“We keep being driven by these overcharges,” Ms. Wilson said. “What are our options here? We really don’t have any options.”

“I feel like we’re held hostage,” Barnstable governor Robert Jones said. “But I don’t see any getting out of it.”

Governors also pressed senior managers to call in some $700,000 in project credits owed by the contractor. Ms. Tierney vowed that the board would push back on further change order requests.

General manager Bob Davis said he would work with Cashman to account for the project credits. “We will push back,” Mr. Davis said. He also noted that despite the change orders, the project remains under budget.

“It’s not as though these [change orders] aren’t being reviewed. They are being reviewed and vetted prior to the point of coming to the board,” Mr. Davis said.

In other business, boat line treasurer Mark Rozum reported that traffic and revenues through February were nearly at expected levels.

“Our fund balances, at this point, at the end of February, are in relatively good shape,” Mr. Davis said.

At the close of the meeting governors went into executive session to discuss pending litigation in both Barnstable and U.S. District Court.