The senior CPI-M leader in a Facebook post reminded India that it had always supported the Palestinian cause.
"The Zionist aim is not only to establish a Jewish nation but also to completely wipe out Palestine," the chief minister said.
He said it was difficult to accept the idea of a united fight against terrorism with Israel.
"India has also always opposed Israel's policy of oppression and Modi has taken a turnaround on that policy," Vijayan said.
The BJP-led government's strategy reflects the "hate politics it practises in the name of religion and food," Vijayan added.