The discovery led to long delays for passengers in the UK and France.
The freight train from the Frethun yard stopped near the tunnel entrance on the French side, Eurotunnel said.
The company said several other people were found on the halted train after it was searched by police and security staff. Those found were returned to France.
A Eurotunnel spokesman said: "A suspicion of migrants on a freight train led us to stop and search the train.
"We decided to stop it just at the entrance to the tunnel."
The company said a "number" of people were found on the train, but was unable to confirm how many.
By Tomos Morgan, BBC News, Calais
We have been hearing rumours from the camp that some migrants have found success crossing over into the UK through the Channel Tunnel.
And the suspicion is, those reports are based around the Frethun freight yard. It is located between the terminal and the tunnel's entrance.
Eurotunnel has earmarked Frethun as a potential weak spot on the line in the past - there are no fences protecting its perimeter.
On Thursday, when Home Secretary Theresa May visited Calais, Eurotunnel asked for increased security at Frethun.
On Friday we saw two migrants being detained in broad daylight right next to the track.
This is just another example of the desperation of these migrants to get into the UK - so additional security would have to be reinforced if authorities want to completely deter migrants from crossing over illegally into Britain.
After the train was moved out of the tunnel, the rail operator said it was working to get services back to normal.
Latest travel reports said vehicle passengers in the UK faced a 60-minute wait before check-in at the Folkestone terminal in Kent and a three-hour wait after that.
Travellers in France were also facing a two-hour wait and passengers without reservations were not being accepted.
Lorry drivers have been warned their journeys from check-in to arrival would take about five hours.
Eurostar said its services from St Pancras International and Ashford were being delayed by about 30 minutes.
Cher Williams, who is travelling to Dordogne in France, said passengers were told the delay had been caused by a broken-down train.
A Eurotunnel freight train had to stop in the Channel Tunnel after a migrant was seen on wagons bound for the UK.