The northbound carriageway between junction 39, near Denby Dale Road, and junction 38, near Woolley will remain closed until at least 6pm.
Diversions have been put in place but drivers have been advised to find alternative routes.
One lane of the southbound carriage way at junction 39 is also closed.
A spokesman for the Highways Agency said repairs to the motorway barriers had been completed and it was hoped the motorway could be fully re-opened by 6pm.
The motorway has been closed since 10.25am this morning (Tuesday) when a car transporter shed its load of nine vehicles.
Some of the cars ended up on the southbound carriage way and other cars slipped down the embankment.
Chief Inspector Paul Hepworth said: “We would ask drivers to be patient when travelling near to junction 39 of the M1 following an accident in which a car transporter lost its load of nine cars earlier today.
“Lane three of the southbound carriageway remains closed while work is carried out to repair a barrier.
“The northbound carriageway is completely closed between junctions 38 and 39 - traffic is being diverted.
“There will be some delays. We are estimating that this carriageway will not reopen until into rush hour or after rush hour.”