Lines between London St Pancras and London Blackfriars are blocked, because of “a number of incidents”.
Thameslink trains were brought to a standstill after a failure to the electricity at London St Pancras earlier on Friday, but it is unclear if this is still the issue.
National Rail expects this disruption to continue until at least 5pm.
Southeastern trains through New Cross were facing heavy disruption for the whole of Friday morning but this has cleared up now.
It comes after a week of tube stations being periodically shut on different days, when Customer Service Managers who are members of the TSSA union walked out on strike.
Two Tube stations were still closed early on Friday morning, after TSSA members walked out in strike on Thursday night.
Bermondsey and Borough were shut “due to the unavailability of staff” but both have since re-opened.
