But the World Health Organization in 2015 classified glyphosate as "probably carcinogenic to humans". But he said a reasonable jury could conclude, based on the findings of four experts he allowed, that glyphosate can cause cancer in humans.
"Throughout much of this case, the plaintiffs seem to have operated under the assumption that they can clear the general causation hurdle simply by showing that IARC's decision to designate glyphosate a probable human carcinogen is scientifically sound", he said.
Before issuing his ruling, Chhabria spent a week in March hearing dueling testimony from epidemiologists.
"Moving forward, we will continue to defend these lawsuits with robust evidence that proves there is absolutely no connection between glyphosate and cancer", Monsanto Vice President Scott Partridge said in a statement.
More than 400 lawsuits were filed before Chhabria's court. The agency noted that scientific studies from other countries concluded the same.
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A key to Johnson's case will be convincing jurors that Monsanto's pesticide - whose main ingredient is glyphosate, a substance some say is dangerously carcinogenic - is responsible for the illness. Farmers in California, the most agriculturally productive state in the US, use it on more than 200 types of crops.
A separate trial is under way in San Francisco in a lawsuit by a school groundskeeper dying of non-Hodgkin's lymphoma - the first case a jury has heard alleging Roundup caused cancer. Wisner says a large part of Johnson's job was to spray Roundup - often 50 to 60 gallons at a time.
In 2014, Johnson was diagnosed with non-Hodgkin's lymphoma, a cancer that affects white blood cells. Homeowners, meanwhile, used Monsanto Roundup on their lawns and gardens. Wisner said Johnson read the label carefully and even contacted the company after developing a rash, but was never warned it could cause cancer. Photos of Johnson presented in court showed lesions in his body.
George Lombardi, an attorney for Monsanto, said non-Hodgkin's lymphoma takes years to develop, so Johnson's cancer started well before he began working at the school district.
Another federal judge presiding over hundreds of lawsuits like Johnson's is deciding whether the claim that Roundup weed killer can cause cancer is supported by good science.