The local authority said working under tricky conditions such as building on a floodplain and near a national heritage site has led to costs spiralling from £36 million to £49 million.
"The new bypass is being built across an area of poor ground conditions, which have been even worse and more unpredictable than expected. Building across a flood plain and poor fenland soils has resulted in large amounts of additional work and material being needed," the council said.
"The depth of the foundations for the river viaduct is two thirds the height of the Cathedral – much more than expected. Also, as Ely Cathedral is a national heritage site, a unique, specially designed viaduct needed to be created which has given the team significant challenges."
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The council said it is now working with contractor VolkerFitzpatrick to minimise any additional costs.
However despite financial issues, the development has passed several major milestones. Construction on the eastern, central and western embankments is now complete, while the abutments, which is where the bridge starts and ends, and the central pier over the railway are also finished.
In addition, steel beams weighing up to 350 tonnes each, which form the bridge decks, have now been lifted into place.
Cllr Ian Bates said: "We all took the brave decision to procure the contract early to get the scheme off the ground and the cost of the scheme is the reality of building in such a difficult area.
"Although this increase in costs is disappointing, we are clear the costs would have been much the same if we had waited, but we wanted to push ahead and get the road built as soon as possible. If we hadn't taken that decision, the project would have been delayed a further 12-18 months and funding may have been lost.
"We have a good working relationship with our contractor and construction is progressing well. We're all working hard to achieve the best result and get the new road open as soon as possible."
The new road is expected to open in October 2018. Once the bypass has opened, the existing underpass at the low bridge will be improved for pedestrians and cyclists.
(LM/MH)
