The privately-operated Huey helicopter was brought in by the Canal & River Trust to stop water coming through a section of the Aire and Calder Navigation, which gave way on Sunday.
It is hoped the operation, which will also involve making the temporary repair water-tight using 150 tonnes of clay brought in by barges, will be completed by Christmas Eve.
The flooding has affected land near West and East Cowick, where 100 properties were flooded in the wake of Storms Dennis and Ciara 10 months ago.
A major multi-agency response swung into action following the "significant breach" of the left bank of the Aire and Calder Navigation near the River Don at New Bridge.
Two flood warnings remain in place and Back Lane is closed.
The Environment Agency's website is still urging drivers to avoid low lying roads near rivers and the canal, which may be flooded.
Three culverts have been blocked off to prevent water heading to the village, but properties closest to the drains "may still be at risk", the EA said.
A spokesman for the CRT said: "The helicopter has been working all morning. It will be working today and tomorrow to reinforce the bank.
"As soon as the bags are in place they will reinforce it with 150 tonnes of clay which we are going to put around the bags to make it water-tight and the water levels in the canal will be able to rise."
A temporary track is being laid across fields to the bank which will allow machines on to carry out a permanent repair.
"Obviously the waterways are 200-years-old and it is a big working network. We do have to be prepared for things like this and we do have contingencies," the spokesman added.