In a tweet, Southern said all lines have been re-opened, but 'residual delays are expected' to and from Portsmouth Harbour, 'due to passengers causing a disturbance on a train' at around 10.20am.
According to National Rail's website, trains remain 'severely disrupted' due to the significant amount of congestion that accumulated whilst the line was blocked.
It comes after it said it was 'advised that passengers have caused a disturbance and assaulted a member of staff 'on a South Western Railway service in the Havant area.
"This has caused disruption to services due to the train involved now coming to a stand, to allow the emergency services to attend and provide assistance to the member of staff," it added.
"The affected train is has now terminated at Hilsea, and when it is safe to do so, will proceed empty to depot to allow services to freely move again throughout this area."
At 11am, services were unable to move out of the Portsmouth area and Southern said trains may be cancelled, revised or delayed by up to 45 minutes.
"A normal service is expected to resume by 2pm," it added.
"South Western Railway and Southern have agreed mutual ticket acceptance between Portsmouth and Southampton Central.
"South Western Railway customers may also use Stagecoach Bus number 21.
"Train service managers are now working hard to restore train services back to the working timetable."