If a judge accepts the agreement, it would be a significant victory for Gov. Jerry Brown and other supporters of what would be the nation's first high-speed rail system.
Voters approved issuing $10 billion in bonds for the project in 2008, but public support has dwindled in recent years as the project's costs have soared.
The proposed settlement was submitted Thursday to a Sacramento County Superior Court judge, a day before a scheduled hearing on the merits of the case, said Anja Raudabaugh, executive director of the Madera County Farm Bureau, lead plaintiff in the case.
The Farm Bureau and other groups representing farmers whose land is in the path of the proposed train sued the authority last year, claiming officials failed to follow the complex California Environmental Quality Act as they planned the route.
An official with the high-speed rail authority confirmed the settlement and requested anonymity because the person was not authorized to discuss the case until a judge approved it.
Details of the settlement were not immediately available.
Rob Wilcox, a spokesman for the rail authority, did not immediately return telephone and email messages.
The farm groups had previously sought a preliminary injunction that would have halted work while the case was being heard, but Judge Timothy Frawley denied the request last November. He said it appeared the California High-Speed Rail Authority acted reasonably and in good faith in trying to follow the state environmental laws.
That decision was an early indication that he might not think the farmers would prevail.
The rail authority had previously reached settlements in some of the other dozens of legal claims against the project, and earlier this year won a separate lawsuit filed by the San Francisco Bay area city of Atherton over its environmental review.
It still faces a 2011 lawsuit from Kings County that claims the state's plan violates the terms of the voter-approved bond measure because not all the track would be electrified.
Construction is scheduled to begin in July on the initial 30-mile segment from Madera to Fresno, in the heart of California's main agricultural region.
The rail authority has been buying land along the proposed route and performing site surveys, engineering design work and geological testing. Officials this month announced that a joint venture's bid of just under $1 billion had emerged as the top bidder.
The Central Valley farmers had hoped to stop the rail authority from planning and engineering work because of their claims that the authority did not thoroughly weigh the potential environmental harms of the project.
The authority argued in court that the potential harm to the state for halting the massive transportation project was far greater than the objections of Central Valley farmers and landowners. The state stands to lose up to $3.2 billion in federal funding if the bullet train fails to meet the federal deadlines, as well as higher construction costs from a delay.
Frawley said in November that he agreed the state had more to lose if the project were temporarily stopped.
Lawmakers approved the first phase of the planned 800-mile line last summer, allowing the state to begin selling $2.6 billion in bonds for construction and tap $3.2 billion from the federal government.
The money is contingent upon completing the first phase of the project by 2017, requiring what officials say is an unprecedented construction pace.
In one of court filing, opponents said rail officials are spending furiously because they hope "to become so financially committed to the currently conceived section alignment that it will be unthinkable to later choose another course."