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PILLAR POINT HARBOR — Harbormaster Robert Johnson’s sudden resignation has set tongues wagging in Princeton-by-the-Sea and left Pillar Point and Oyster Point harbors without a clear chain of command.

Johnson’s last day on the job was Sept. 10, but he is still on the payroll on paid vacation leave until Dec. 31.

Johnson, 59, had been harbormaster at Oyster Point Marina since 1989. He was conscripted to take over the role of harbormaster at Pillar Point in January 2010 to replace Dan Temko, who had retired. The decision not to replace Temko saved the San Mateo County Harbor District $161,000 a year but created a double workload for Johnson.

In April, the harbor district commission voted to continue the arrangement despite a staff report that described it as less than ideal. The report noted low morale among harbor district staff, who have foregone raises for several years and are chronically understaffed due to vacations and sick leave.

It’s now unclear whether the harbor district will promote one or two harbormasters from within its ranks or look outside for a replacement. The district started the fiscal year with a $1.4 million deficit.

District General Manager Peter Grenell did not return repeated calls for comment.

Reached by phone this week, Johnson wouldn’t explain his reasons for leaving. But he said he was proud of what he and the crew at Pillar Point Harbor accomplished together, finishing many harbor improvement projects that had been sitting on the back burner for a while.

“I’m a person who can take a project to completion,” Johnson said. “I inherited four years of deferred maintenance when I came to Pillar Point.”

More projects await his successor. The main pier, built in the 1970s, is aging, and the fishing pier to the west of the harbor has erosion damage.

Harbor district staff recently described a major problem with the public trail leading to Mavericks beach, which needs repairs.

The district recently raised berth fees to help pay for projects like these.

It also tacked another $10,000 onto an event permit fee for the Mavericks surf contest, over the objections of Jeff Clark and his organization.

The total permit fee is now $30,000.

Meanwhile, the district’s budget may soon be maxed out by an expensive plan to build a new retaining wall and office complex at Pillar Point that could house an educational nature center and some marine research facilities.

Contact Julia Scott at 650-348-4340.