"There are some serious dick-heads out there," they said.
Bike Auckland spokeswoman Jolisa Gracewood said as far as they know, nothing like this had happened before.
"Whether mischievous or malevolent, it's a silly and dangerous thing to do, and someone could have been seriously hurt ... we firmly hope it's a one-off.
"Hundreds of people enjoy riding the Northwestern Cycleway across the causeway every day without incident and value this safe route enormously.
"It's a jewel in the cycle network since being upgraded a couple of years ago, and especially at rush hour is often the fastest way into and out of the city," she said.
Auckland Transport spokesman James Ireland told the Herald they want everyone to be safe when using cycleways.
"Putting rocks across a cycleway is incredibly dangerous and irresponsible.
"We are glad no one was hurt. And if anyone sees anything like this in the future please get in contact with AT straight away," he said.