A witness called Mark said the vehicle abandoned on the bridge appeared to be a silver taxi.
"There's a whole lot of police and rescue workers looking skyward," he told 2GB.
However it remained unclear if the man was a passenger in a taxi and had ordered the driver to pull over before getting out and climbing the southern pylon, or was driving.
It appeared the man had climbed one of the pylons on the Milsons Point side.
The Transport Management Centre confirmed to news.com.au that two city-bound lanes were closed "following reports a pedestrian was seen walking on the deck of the bridge".
A spokesman for the TMC said three lanes were closed as police took part in the
operation to bring the man to safety.
"Lanes were closed which caused significant traffic delays in both directions," he said.
"As police are still at the scene we advised motorists to continue to avoid the area."
He said buses were terminating at Macquarie Park and North Sydney and commuters can finish their journeys into the city by train.
NSW Police confirmed the bridge has now reopened after the man remained climbed on a pylon and remained there for around 90 minutes.
Police said they were called to the scene after reports a man was trespassing on the bridge and confirmed he had climbed up and refused to come down.
"A police operation was launched, with the assistance of Police Rescue, Police Negotiators, Traffic and Highway Patrol Command, and the Motorcycle Response Team," a spokesman said.
"About 10.50am, the man climbed down and was arrested."
The man was treated by paramedics at the scene and was taken to Royal North Shore Hospital for assessment.
