A grey Sunday is on the cards after the National Environment Agency (NEA) forecast thundery showers to blanket many areas in the late morning today.

This comes on the heels of yesterday's wet afternoon.

What had begun as a sunny morning was overshadowed after lunch by ominous thunderclaps that roared over the island, accompanied by flashes of lightning.

This prompted the NEA to tweet multiple warnings of heavy rain with gusty winds over many parts of Singapore.

By late afternoon, Paya Lebar Road and Leng Kee Road came close to flooding.

But train commuters were the worst affected. At about 5.35pm yesterday, SMRT first tweeted about a disruption between Bishan and Toa Payoh MRT stations, but it later said train services between Ang Mo Kio and Marina South Pier stations in both directions were disrupted.

This was after a trackside fire in the tunnel between Marina Bay and Raffles Place MRT stations was detected at 5.55pm.

The affected section of the North-South Line cuts through the heart of Singapore's tourist district, including stations such as Orchard, City Hall and Dhoby Ghaut.

As traffic became heavier in the shopping belt, traffic police officers were spotted assisting at the junction of Stamford Road and North Bridge Road.

Commuters were seen checking their mobile phones, looking for a shared ride.

Near Braddell MRT station, Dr Jeremy Chan was heading back to Serangoon after closing his clinic for the day when he got caught in the delays. But he complimented the SMRT staff for giving him directions. He said about the disruption: "I'm not upset by it, it's usual to have delays."

At City Hall MRT station, commodity manager Tan Yean Shi, who lives in Yishun, said that while the detour was "a bit troublesome", she was not angry because breakdowns are now a common occurrence.

"There were people (assisting) inside the station and outside. It's not bad, they're quite helpful," said the 33-year-old.

Sales executive Imelda Tan, 51, was at City Hall MRT station when she was instructed by SMRT staff to take the Circle Line to Bishan, and catch a bus from there to her home in Braddell.

"I live in an area quite far from a bus stop, so I don't know if I can take a bus from Bishan. I may have to take a taxi and pay more - if I can find a taxi," she added.

She said staff were on hand to assist during the train breakdown, which helped.

Snaking queues formed at several bus stops as the heavy downpour continued late into the evening.

In July 2015, a massive rail breakdown was caused by a leak near the Tanjong Pagar MRT station tunnel, which over time created salt deposits on an electrical component, leading to several electrical trips along the East-West Line as well as the North-South Line.