Trains are being cancelled or delayed by up to 50 minutes after overnight engineering works between Bognor Regis and Barnham were not finished on time.
Southern Rail said fewer trains were able to run and that the disruption was expected until 9am.
Passengers are being advised to travel from Barnham instead of Bognor Regis where possible.
Replacement buses will be running between the two stations.
Commuters trying to reach London from Bognor Regis are also affected.
A Southern Rail spokesman said: "Network Rail have confirmed that planned overnight engineering work in the Bognor Regis area has overrun, and engineers require an additional 90 minutes to carry out final testing.
"During this time, part of the signalling system will remain switched off and train crew will be verbally guided through the affected signals by the local signaller for this area."