Long lines of vehicles on the Causeway around 6pm on 18 December 2015.
Local transport companies and travel agencies said the buses hit the highways, which are not affected by the recent floods.
Eight districts in the state of Johor have been hit by floods, which have also affected other states including Pahang and Kelantan.
A spokesman for Konsortium Express and Tours said their coaches have managed to minimise unnecessary delays by avoiding areas in Johor that were affected by the floods.
Konsortium, which runs 10 to 13 coaches a day into Malaysia, said buses take the highways, bypassing Johor, en route to popular destinations such as Malacca and Kuala Lumpur.
While flood waters may not slow down the buses, demand, wet weather and the long weekend will, said the transport companies.
Some transport companies have increased the number of coaches to meet the higher demand. This is likely to worsen congestion from Singapore to Malaysia, a spokesman for BSB Express Transport said.
BSB Express Transport has added two more coaches travelling from Singapore to Malaysia during the Chinese New Year period.
Mr Christopher Chia, director of Travel Delightfully, said the travelling time could even be 2 ½ hours longer than usual, especially if there is an accident along the route. It now takes about five hours to complete the journey from Singapore to KL.
According to the Malaysian Meteorological Department, afternoon thunderstorms are expected to continue in most states, although they are likely to subside in the next week.
To counter any unexpected delays, tour agencies and transport companies have prepared contingency measures.
BSB Express Transport said that back-up coaches are on standby, while Konsortium said that it would reroute its coaches in advance.
Most of them informed customers of the higher likelihood of delays during the Chinese New Year period prior to booking and urged customers to be understanding.
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