The filmmaker has posted footage of the storms in his latest behind-the-scenes video blog from the set of the top secret movie, which has been shot across his native New Zealand for the past eight months.
Jackson explains he was shooting scenes of dwarves floating down the Pelorus River for the second sequel when blue skies clouded over and the weather took a change for the worse.
In the taped video footage, he says, "Our location shooting came to a pretty dramatic end because the police arrived and said they were about to issue a severe weather warning. I've never seen a crew pack up their gear so quickly.
"The very next day, everywhere where we were standing... was under floodwater. That was incredibly dramatic. The rise of the river level was, like, 20 or 30 feet."
Jackson and his crew also faced adversity when they shot scenes on the slopes of Mount Taranaki - they had to create an elaborate scaffolded walkway for the cast so ancient vegetation growing in the world's second oldest national park wasn't disturbed.