Eurotunnel said services were delayed and cancelled after migrants attempted to access restricted areas on the French side.
The incident caused a return of queues on the M20 in Kent for lorry drivers trying to cross the Channel after Kent Police reintroduced Operation Stack.
It also prompted renewed calls for authorities to act to solve the worsening Calais migrant crisis, which is costing the UK economy millions of pounds.
The Fresh Produce Consortium estimates that £10 million of fresh fruit and vegetables have been thrown away since the start of the year as a result of the problems.
A Eurotunnel spokesman said the incident was affecting freight traffic only, with passenger services running to a full timetable.
He said: “Eurotunnel reiterates its call to the authorities to provide a solution to the migrant crisis and restore order to the Calais region.”
The Port of Dover, which faced heavy disruption this week due to striking ferry workers in France, said it remains “open for business”.
A port spokesman said P&O Ferries was operating a full Dover-Calais service, while DFDS Seaways was running full services to Dunkirk.
The return of Operation Stack - where freight traffic is queued on sections of the M20 - came hours after police lifted all phases of it.
Kent Police said: “Op Stack phase 2 implemented due to disruption at Channel Tunnel. M20 closed coast-bound 8 to 9.
“Non-freight traffic now being allowed into Channel Tunnel terminal. M20 Junctions 11 to 12 no longer closed but delays likely. Check with operator if heading to Channel Tunnel as services disrupted.”
The migrant crisis in Calais has been escalating in recent weeks, with around 3,000 people displaced from countries including Eritrea, Syria and Afghanistan setting up camp near the port.
Migrants have been taking advantage of slow-moving and queuing traffic by trying to board UK-bound vehicles, forcing some drivers to take long detours to skip Calais altogether.
Home Secretary Theresa May and her French counterpart Bernard Cazeneuve this week agreed to increase the joint intervention fund to improve security around the port and the Channel Tunnel.
French aid workers have reported a “catastrophic” situation, with predictions that 2,000 more migrants could arrive over the summer at the camp, dubbed Jungle II.
Volunteers from l’Auberge des Migrants say up to 50 new migrants were arriving every day at the camp, and there were not enough tents, blankets or food.
British travellers have been advised by the Foreign and Commonwealth Office (FCO) to keep vehicle doors locked in traffic and when unattended in Calais.