Passengers on Auckland train services were told to get off their trains and find their own way to their destinations as services across the city were shut down following a bomb threat in the capital.

Commuters in both Auckland and Wellington should expect delays and cancellations to train services this afternoon and during evening rush hour, after services were shut down during a threat to the National Train Control Centre.

Nothing untoward was found, police said, following a search of the Wellington Railway Station, which houses the control centre, and services are running again. But passengers should expect delays.

A woman told the Herald she and other passengers were forced to get off their train when it was shut down at Homai station in South Auckland.

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"They opened the doors and said 'we've been suspended, we don't know what it is, we've got a red light'," she said.

"The security staff said it was related to Wellington as it had been evacuated, that's why the Auckland network wasn't running."

Everyone on board exited the train and were forced to find their own way to get to their destinations, she said. Luckily, her partner was able to pick her up, she said.

Metlink in Wellington said a police emergency forced an evacuation of the capital's central station. The National Train Control Centre is located at Wellington Railway Station.

The station has re-opened and services have resumed.

"However, please expect delays and cancellations across the network as we get services back up and running," Metlink said.

"This will likely have an impact of this afternoon's peak services," the travel operator said.

"Please keep checking the service update for more information as it becomes available."

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However, rail tickets would be accepted on regular Metlink buses.

In an update, AT said trains were running again after being suspeded earlier this afternoon due to the evacuation.

"National Train Control is operated out of Wellington and the evacuation meant trains were stopped or moved to the nearest platform while KiwiRail activated its alternative train control system," AT said in a statement shortly after 4pm.

"Auckland services will run at a 20 minute frequency during afternoon peak, so commuters may experience some delays."

A threat was made at Wellington Railway Station around 1.50pm, a police statement said.

One man said his train was stopped and the driver announced it was because of a bomb threat at Wellington Station.

The driver told passengers emergency services were doing a sweep of the building, the man said, and all trains in and out were stalled in the meantime.

Police said nothing untoward was found at Wellington Railway Station, which has since re-opened.

"Wellington Railway Station has been re-opened following a threat made this afternoon," police said in a statement.

"The location was found to be safe and we would like to thank members of the public for their patience."

KiwiRail chief operating officer David Gordon said the Wellington Railway Station, including the national train control centre, was evacuated for a short time this afternoon.

"All trains were stopped or moved to the nearest platform across New Zealand, including in the Auckland and Wellington metro areas, while we activated our alternative train control system."

For further information about the evacuation, please contact the police, Gordon said.

On it's website, KiwiRail said the centre was kept secure and locked off to the public to protect "passengers, employees and customers from any potential high-security problems".

"We also have a standby disaster recovery centre in Palmerston North which can provide Train Control to continue to function in the event of an emergency situation or disaster in Wellington."