Until the cells were found in test samples taken at six sites on the Tongariro, Whakapapa, Mangatepopo and Whanganui rivers, the pest was thought to be confined to South Island rivers.
Further investigations found no evidence of live didymo in the North Island rivers.
But an audit was held to establish how the dead cells showed up in surveillance samples.
Niwa chief executive John Morgan said yesterday the answer was that lids on water-sampling containers staff used in river testing had been contaminated with dead didymo cells.
The contamination occurred when the lids were in a South Island laboratory where dead didymo cells had been weighed during scientific study.
When Genesis Energy assigned Niwa to test rivers it used to drive electricity turbines, the contaminated testing vials were brought north.
Biosecurity Minister Jim Anderton said rigid laboratory hygiene meant live didymo cells could not have been transferred to the North island.
Fish and Game chief executive Bryce Johnson said last night: "Everyone makes mistakes and we must learn from the huge consequences of this one.
"It caused an amazing reaction that cost time and worry for heaps of people."