Freight trains may be ready to roll again on the Northwestern Pacific Railroad, but a dispute between two public rail agencies threatens to sidetrack the cargo service.

North Coast Railroad Authority, which oversees freight trains, and Sonoma-Marin Area Rail Transit, which owns the tracks south of Healdsburg, can't agree on joint operating rules.

"I don't know when I'm going to be able to do anything," said John Williams of NWP Co., the private company picked to run rail cargo service in Sonoma, Napa and Marin counties.

Williams said NWP Co. could have freight trains running between Napa County and Windsor by the end of the year if it gets the go-ahead.

So far, however, SMART and NCRA are deadlocked on the railroad operating agreement, which will determine how commuter and freight trains jointly use the tracks.

SMART plans to run commuter trains in Sonoma and Marin counties starting in 2014.

"We put forward reasonable terms. They have not accepted," said Chris Coursey, spokesman for SMART.

"The timing is in their hands," said NCRA executive director Mitch Stogner. "We are on the one-yard line."

The issue could come to a head Wednesday when representatives of NCRA and NWP Co. appear at a SMART meeting in Santa Rosa. The meeting starts at 1:30 p.m. at the Sonoma County Board of Supervisors chambers.

While SMART owns the tracks, NCRA has spent $68 million repairing them for cargo trains.

Freight service on the Northwestern Pacific has been halted since 2001 when U.S. rail regulators ruled the storm-damaged railroad was unsafe for train traffic.

NCRA began repairs in 2005 and chose NWP Co. in 2006 to provide the freight service. NCRA said cargo trains will provide a low-cost alternative for shippers and take trucks off Highway 101.

With repairs almost complete, NCRA and NWP Co. are ready to ask the Federal Railroad Administration to reopen the line, Williams said.

But the federal agency ruled last month that cargo service can't resume without SMART's approval. And SMART says the freight trains shouldn't run until there's an operating agreement.

SMART and NCRA have been negotiating for two years, but they've reached a stalemate over issues including insurance, shared costs and operating schedules. There's also disagreement about how SMART will work on the tracks while freight trains are running.

In a memo to the SMART board Monday, general manager Lillian Hames said the agency shouldn't give its approval for freight service until its concerns are addressed in a new operating agreement.

She also recommended that SMART not approve NWP Co. as the freight operator if there's no accord.

Meanwhile, NCRA and Williams are asking the Federal Railroad Administration to reverse its decision giving SMART veto power over cargo trains. They said shippers will be hurt if freight service is delayed.

Officials at the federal rail agency weren't available for comment.