The nappy and wet wipes manufacturer said it failed to meet the UK governments deadline to remove plastics from wet wipes by mid-2026.
The factories, which make a range of paper products, will close in 2025 and the manufacturing site of bathroom wipes at Kimberly-Clark will move to Germany.
Trade unions body, United, condemned the decision and called for extra time, telling BBC News the closure would be "catastrophic" for the town.
Kimberly-Clark said in a statement it was: "no longer viable to keep our consumer and B2B sites operational".
Sharon Graham, Unite's General Secretary said: "Unite will fight to reverse this decision and calls upon the government to intervene to try and save these vital jobs. This decision, taken so rashly, cannot be accepted."
Unite has called for more time for manufacturers to produce environmentally friendly alternatives to avoid job losses.
Kimberly-Clark said: "While phasing out plastics from our baby wipes is a key part of K-C’s sustainability plans, it isn’t possible to adapt our manufacturing processes in Flint in time.
"Decisions that involve our employees are the hardest to make and we know this is a challenging period for our team."
