The train was stopped in the Channel Tunnel at about 15:30 BST on Sunday and Eurotunnel later reported delays of more than three hours.
Eurotunnel said the train was stopped and searched after an alert was raised. The migrants were taken into custody.
It was the second time in three days a freight train has had to be stopped in the Channel Tunnel due to migrants.
The latest incident involved a national network rail freight train heading for Kent from the SNCF Reseau track in Frethun, France.
Eurotunnel initially tweeted that its service was "operating with delays due to a National Freight train stopped in the tunnel".
Almost three hours later it said: "Due to the stopped National Freight Train, there is a 3.5hr wait for our Passenger service from France; from the UK, a 1hr wait on site."
Then at 19:00 BST it reported that the train had exited the Tunnel and work was under way to reform the timetable and reduce delays.
A Eurotunnel spokesman said: "The search was conducted by the Police aux Frontiers and security staff.
"The migrants found have been taken into custody by the French Police aux Frontieres in France, and the train sent back to the SNCF yard at Frethun.
"We apologise for any inconvenience caused by this incident."
Eurotunnel said it was was working on restoring full service.
Last week the operator said extra security measures were making a "real difference" and the number of migrants trying to get into the Eurotunnel terminal near Calais had fallen to about 150 a night.
That number had peaked at 2,000 at the end of last month.
Eurotunnel passengers have again faced delays after migrants got on to a freight train bound for the UK.