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Operation Brock will start today, despite high level crunch talks raising the possibility of Brexit postponement.
Weekend closures were experienced by motorists using the M20 near Ashford while last minute preparations were put in place.
KMTV report on latest M20 restrictions
The contraflow system between Junctions 8 and 9 of the M20 was due be operational from 6am, despite the Brexit deadline now being undefined, but work overran and the stretch remained closed until 7.30am with traffic building up as a result.
The controversial plan could have been postponed at a meeting on Friday.
There had been fears that implementing the measures could cause frustration for drivers and may impact half-term holiday traffic heading to the Channel ports.
A series of closures were implemented on Saturday and Sunday in an effort to put Brock in place in three days.
A spokesman for Highways England said: "The M20 will be closed in both directions between Junction 7 (for Maidstone) and Junction 9 (Ashford) overnight tonight and tomorrow night from 8pm until 6am each night.
"Saturday night’s closure may be cancelled depending on how much work can be completed on Friday.
"On Sunday night, the coastbound carriageway only will be closed from 8pm between junctions 7 and 9, reopening at 6am on Monday, with the contraflow up and running."
When Highways England introduced the restrictions earlier this year ahead of the original Brexit deadline of March 31, they triggered a wave of protests and complaints, particularly about the narrowness of the lanes used for the contra-flow.
Under the scheme, the coastbound side of the motorway between Junctions 8 and 9 will be used only by HGVs heading to Dover, with all other traffic restricted to a 50mph contraflow system on the London-bound carriageway.
In April, Highways England lifted the restrictions when the Brexit deadline was pushed back until the end of October, but the steel barrier on the London-bound stretch has remained in place ever since and the contraflow will be reintroduced next month.
Earlier this year, KentOnline revealed how hundreds of drivers of foreign-registered vehicles got away with speeding on the M20 contraflow.
Police said they did not pursue motorists from other countries who exceeded the temporary 50mph limit because officers were unable to identify them.
The major J10a scheme has also been pushed forward to allow access to its coast-facing slip roads ahead of the original October 31 deadline.
