The protesters, backed by Greenpeace, marched into ECan's Lichfield street building about 8am today.
They held banners asking for our rivers to be saved from the intensification of dairy farming and for democracy to be reinstated to the regional council - ECan's councillors are a mix of government appointees and elected officials.
ECan chief executive Bill Bayfield told police the protesters did not need to be moved on.
"We've had good interaction with the protesters and we respect their views," he said.
ECan communications manager Katherine Trought said the council knew it was a likely target for protesters.
It was the third protest in recent weeks related to water issues in Canterbury. Last Thursday, several Greenpeace protesters were arrested at the site of the Central Plains Water irrigation scheme, near Springfield, after trying to occupy the basin of the dam.
Event organiser and Greenpeace water spokeswoman Genevieve Toop said New Zealand faced a water crisis - seven out of 10 rivers were unswimmable and water irrigation schemes would make things worse.
"More water means more cows, which means for dirtier rivers."
Toop said cow numbers in Canterbury had doubled since 2011.