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It is the latest job loss blow to the area following the closure of the nearby oil refinery in April last year, which also resulted in the loss of about 400 jobs.
In March, bus manufacturer Alexander Dennis announced plans to close its Falkirk plant with 115 roles lost.
The UK government, under then-Prime Minister Sir Keir Starmer, previously pledged an additional £200m in funding for Grangemouth from the National Wealth Fund.
Flynn said the Scottish government had "strongly opposed" Syngenta's plans.
He said he would continue to press the UK government on the £200m funding pot.
"My thoughts are with the workers, their families and the local community who will be affected by this decision," he said.
"We made clear to Syngenta's board our strong opposition to any potential scale down or closure of their Grangemouth site."
Flynn added: "During this period of consultation, I sincerely hope that the UK government will now provide some of the £200m committed to Grangemouth, since not a single penny has yet been allocated from that fund promised in 2024."
The Scottish Green Party co-leader, Gillian Mackay, said the move was another "devastating blow" for the area.
"Our governments should be doing more to protect jobs and ensure that workers can benefit from our transition to a greener future," she said.
"Grangemouth is my home, and I am concerned about what this will mean for the local community if it goes ahead."
