Channel Tunnel services are running to schedule again after about 120 migrants broke into the terminal on the French side on Friday evening.
Trains between Folkestone and Calais were suspended overnight into Saturday then delayed during the day after migrants broke through security fencing.
One Eurotunnel employee and two police officers were injured in the incident.
Eurotunnel warned freight journeys from Calais were still suffering disruption.
In a statement issued at 00:23 BST on Sunday, Eurotunnel warned freight drivers that the journey from check-in to arrival in the UK would take approximately four hours.
On Eurostar passenger services there had been delays of up to three hours during Saturday morning while all services ran through just one of the two tunnels. But services were running on time again by the evening.
The disruption had affected both Eurotunnel, which runs freight and car services, and Eurostar, which runs passenger trains using St Pancras, Ebbsfleet and Ashford stations.
Eurotunnel said it was concerned there may be another attempt at a breach.
Staff were "being very careful because it was such a different tactic, a different approach" in Friday night's incident, it added.
Trains were stopped from 23:30 BST on Friday after security staff were overwhelmed by the "number and aggression" of the group, Eurotunnel spokesman John Keefe said.
People had gone to the end of new security fencing, installed during the summer months, and broken through older fences. Police were waiting at the tunnel to round up those who reached it, he added.
He said staff were shoved and stones thrown as security fences were breached.
"Services were suspended because of the very large, determined and organised group of migrants who burst through the fence and made their way to the terminal," he said.
French police and British authorities removed people from the area.
The situation in Calais is part of a wider migrant crisis across Europe, with huge numbers of people heading north from the Mediterranean.
Extra security, including fencing, paid for by the UK, started to be put in place in the summer. It is aimed at making it harder for migrants to get onto the platforms and trains heading into the Channel Tunnel.
A man died on Wednesday near the tunnel entrance in Calais - the 13th migrant to die trying to reach the UK since late June and the fourth to have died in September.
- Migrants who are camped in Calais are attempting to reach the UK by crossing the Channel
- In August, Eurotunnel said the number of attempts by migrants trying to get into its terminal near Calais had fallen to about 150 a night, down from a high of 2,000 in the previous month
- The situation in Calais is part of a wider migration crisis in Europe - caused largely by people fleeing war and oppression in countries such as Syria, Afghanistan and Eritrea
- More than 240,000 migrants have crossed the Mediterranean already this year, arriving on the shores of Greece and Italy
Read more: Why is there a crisis in Calais?