Three lanes of the motorway have been shut down on the Thelwall Viaduct, leaving only one lane open.
One lane has also been closed on the northbound carriageway.
National Highways says there are "severe delays" and queueing traffic going south, with tailbacks as far as Junction 22 near to Newton-le-Willows.
The southbound entry slip road at Junction 21 is also closed.
Temporary repair work is being carried out after the discovery of a defective bridge joint.
The lane closures caused two-hour delays on Friday, with queues stretching back 13 miles.
The work is expected to continue until 5pm today.
National Highways explained that today's work will allow them to plan a full repair at a later date. That is likely to mean a full overnight closure of the M6 over the viaduct.