It said while later running trains "may benefit an estimated 140, 000 extra passengers each weekend with their journey home, there are an estimated 55, 000 people that could be affected".
"Engineering works will be taking place this weekend on some routes and customers are advised to check their planned journey before setting out, " a spokesman said.
The command of the shipwrecked Costa Concordia faced mounting scrutiny at the weekend over its handling of the ship's ill-fated journey, which ended in a disorderly evacuation and at least five deaths.
Rail passengers between south Wales and London can expect their journey to take up to 90 minutes longer over the Easter weekend due to work at Reading station.
"Scheduled engineering works will be taking place this weekend on some routes and customers are strongly advised to check their planned journey before setting out, " said a Greater Anglia spokesman.