The Agriculture Ministry said on Tuesday that authorities were investigating suspected fish poisoning at the mouth of the Zalmon River in the Sea of Galilee.
A joint investigation was launched by the ministry and the water authority after hundreds of dead fish were found floating in the area.
Tests were conducted and experts have ruled out any damage to the drinking water system.
The ministry said the public can continue to consume fish, but urged them to exercise caution and buy only from established shops.
The Ministry of Environmental Protection said it was also working with the water authority on the matter and was guiding the Jordan Valley Regional Authority in disposing of the thousands of fish through an authorized company that specializes in handling organic waste.
The Water Authority and Israel Nature and Parks Authority wardens were working together to collect the dead animals, it said.
Channel 12 reported that suspicions were first raised by the Kinneret Research Laboratory, which detected an unusually high mortality rate among fish in the area.
Officials suspect that the fishermen have spread poison in the water. The network noted that similar incidents have occurred in recent years and that in some cases the poisoned fish were later offered for sale in stores.