Groups representing the farmers claimed in lawsuits that the rail authority failed to conduct the thorough environmental reviews required by California law and comply with public meeting laws.
But Sacramento County Superior Court Judge Timothy Frawley ruled the rail authority "acted reasonably and in good faith" of state environmental law.
Approval of the injunction would have prevented the rail authority from buying land along the proposed route and continuing with site surveys, engineering design work and geological testing that began months ago.
Dan Richard, the rail authority chairman, was pleased with Frawley's decision.
"Both the voters and the Legislature have spoken on high-speed rail," he said in a statement. "The judge's decision ensures that we can continue to move forward with our preparatory work to build the first segment of high-speed rail in the Central Valley, with a plan to break ground next summer."
High-speed rail officials said any delays would have set the project back by months and even put $2.3 billion in federal grants in jeopardy.
Lawmakers approved the first phase of the planned 800-mile line this summer. This allowed the state to begin selling $2.6 billion in bonds for construction of the first 130-mile stretch of the bullet train in the Central Valley. That approval also allowed the state to tap $3.2 billion from the federal government.
In 2008, voters approved issuing $10 billion in bonds for the project, but public support for the plan has dwindled in recent years as the project's expected costs have soared. The most recent estimate is at least $68 billion for the completed project linking Northern and Southern California.
The Associated Press contributed to this report.