The NSW Government has vowed to introduce tougher fines for illegally climbing the Sydney Harbour Bridge, with the man who brought the city traffic to a standstill this morning facing a $3,000 fine.

Key points: Some people were stuck in traffic for three hours

Some people were stuck in traffic for three hours The man climbed up the bridge about 4:30am today and was taken into police custody around 9:30am

The man climbed up the bridge about 4:30am today and was taken into police custody around 9:30am At one stage, all northbound lanes were closed to traffic on the Sydney Harbour Bridge

NSW Roads Minister Melinda Pavey said at a press conference today, "you can't stop people doing stupid things" but promised to look at increasing the penalty.

"[You get] $5,500 for jumping the fence at the SCG, you've got a $10,000 fine [for climbing] on the Golden Gate Bridge, upwards of that I'm going to take some soundings on that from the community as well as my agencies," she said.

The man, 43, from Woolloomooloo, was safely taken into police custody at about 9.30am after climbing the bridge morning, with roads through central Sydney slowly returning to normal after the police operation caused traffic mayhem during the morning rush.

The State Opposition slammed the incident as a security breach.

"What was happening today, there were 10 security officers, CCTV and yet one man has brought this city to a complete standstill," Opposition MP Guy Zangari said.

Detective Inspector John Maricic said the man rode a bicycle onto Lane 1 of the bridge, got off his bike, scaled the fence of the rail corridor and climbed a pylon up onto the beams.

The man was over a number of road lanes, which required the closure of roads on the bridge, Detective Inspector Maricic said.

"[It was] incredibly dangerous," he said.

Police lead the man down the Sydney Harbour Bridge, where he had been for around five hours. ( ABC News )

"I was seriously concerned for the travelling public travelling underneath him. I did not want him to fall and come into contact with an innocent member of the public.

"The police negotiation unit were called in and engaged with him for a number of hours … and the male agreed to leave the pylons of the Harbour Bridge."

The man has "significant mental health issues" and his motive was a "based on a family issue", Detective Inspector Maricic said.

Police said charges would be laid today.

NSW Ambulance said he had been taken to St Vincent's Hospital in a stable condition.

Traffic returning to normal

All lanes on the bridge reopened just after 10:00am, and traffic remained badly congested around the Sydney CBD until the late morning.

The man climbed the Sydney Harbour Bridge and was up on the beams negotiating with police for five hours. ( AAP: Mick Tsikas )

Traffic Management Center spokesman Dave Wright said it was one of the worst days for Sydney traffic in recent years.

"Any thoroughfare that came into the CBD was affected," Mr Wright said.

"It was basically at a crawl, you would have been faster getting into the city if you were actually walking."

Multiple northbound and southbound lanes of the bridge were closed during the hours-long police operation.

Traffic was crawling on the city's major road arteries during police negotiations with the man, with the road chaos easing around 11:00am.

Live Traffic NSW reported that traffic had been banked up for southbound commuters all the way to North Ryde — 20 kilometres north-west of the city on the M2 — during the rush hours.

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A knock-on from the Harbour Bridge closures also affected the Anzac Bridge, causing the arterial Victoria Road to be backed up for more than 10 kilometres leading into the smaller bridge.

The City-West Link had traffic issues all the way to Haberfield and the Eastern Distributor was experiencing some delays.

Commuter Zack Jackson said he had been stuck in the gridlock all morning.

"I've been waiting three hours, I've lost half my day's work," he said.

"If I could, I'd do a U-turn and go home but I can't. I've got customers ringing me up and busting me — it's very frustrating."

'We can't wrap bridge in barbed wire'

Trains were not affected by the operation.

Buses were delayed by up to 70 minutes, and several buses were stopping their trips at train stations on the north shore to allow passengers to catch the train.

The Roads Minister said it was difficult to stop people from accessing the bridge.

"Unless you are prepared to wrap the whole bridge in barbed wire, then there is a chance that something like this might happen," Ms Pavey said.

Ms Pavey said she empathised with commuters.

"It's not an easy day — it's not a good day for the Sydney commuter," she said.