The rail operator said at 6.30pm that there were possible delays, cancellations and alterations on Basingstoke-bound trains due to an incident on board a train which blocked the line.
A statement said: "Police are attending an issue on board a train. This means that Basingstoke bound trains will run non stop between Farnborough and Basingstoke."
They later added that "police carried out investigations on a train".
Trains towards Basingstoke were not stopping at Fleet , Winchfield or Hook.
All lines had reopened by 7.10pm but residual delays of up to 45 minutes were expected until 9pm.
Trains were able to run normally but it was warned that some short notice alterations to late running trains may be necessary.
Passengers were earlier told: "If you are at Fleet, Winchfield or Hook and are trying to get to Basingstoke, please travel to Farnborough and change there for a train to Basingstoke.
"If you are trying to get to Hook, Winchfield or Fleet from Farnborough, please remain on the train and change at Basingstoke."
"We are sorry for the disruption to your journey this evening," South West Trains said.