The operator suspended services for a brief period shortly before midnight due to “migrant activity”, adding that French authorities were dealing with the situation.
It tweeted: “Please be assured we always work hard to maintain the highest levels of security at our Calais terminal.”
Le Shuttle, which takes passengers across the Channel in cars, caravans, buses or other vehicles, usually operates up to four crossings an hour.
All services for Saturday are sold out, the website shows.
Journeys from France to the UK are now running on time, with three departures every hour, but passengers in Folkestone are facing waits of up to five hours.
Replying to a passenger hoping to cross on a service just after midday Eurotunnel said: “It’s not easy to estimate how long the delays will take to resolve. We’re all doing our best.”
The first Eurostar service, which carries passengers only, departed on time at 6.18am with all other services running on time, according to its website.
Migrants invading the Eurotunnel terminal in Coquelles has become a nightly occurrence.
There were delays to the service on Thursday when the body of a suspected migrant was found on the roof of a Eurotunnel train at the Chunnel terminal in Folkestone.
The news came as video footage emerged apparently showing migrants travelling to Britain on empty freight train carriages.
An estimated 5,000 migrants displaced from countries including Syria, Libya and Eritrea are now believed to be camped in and around Calais.
Freight transport chiefs said Britain’s freight industry is losing 750,000 a day because of the huge problems lorry drivers have faced this summer trying to cross the Channel.
Operation Stack – where freight traffic is queued on sections of the M20 when cross-Channel services are disrupted – remains in place, and Kent Police warned it could continue until at least tomorrow.
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