This is due to a fault with the signalling system, which was first reported shortly 6am.
"This means that Seaford and Bishopstone station will not be served by trains.
"Services to Seaford will terminate and restart at Newhaven Harbour."
Buses had been requested and were expected to be in place by 8.30am.
Southern added: "In the meantime, please use Brighton & Hove bus services between Seaford, Bishopstone & Newhaven."
However, in an update just before 8pm, Southern said engineers were preparing to run some trains on the line between Newhaven Harbour and Seaford, adding: "These trains will have to run at a slower speed than usual, so journey times will take around ten minutes longer."
It comes after services between Seaford and Lewes were suspended all day yesterday (Monday) due to weekend engineering works, which overran.
Network Rail Kent & Sussex issued an apology on social media just after 8.10am today.
"We're so sorry for the second day of disruption for Southern Rail passengers between Newhaven Harbour and Seaford," its Twitter post read.
"Our engineers have fixed the signalling faults and the line is open. But please continue to check before you travel as it will take time to reintroduce trains."
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