The A16 between Crowland to Spalding opened a fortnight ago but a four-mile section between Peterborough and Crowland remains closed to traffic.
Cracks have appeared in the surface near Car Dyke bridge at Eye Green.
Lincolnshire senior highways officer Paul Coatup told the BBC: “I’m not sure we fully understand the cause of the problem and because of that we’re not able to determine the engineering solution and give any idea about the extra cost or delay it might actually lead to.”
Peterborough city councillor David Sanders said: “This shouldn’t have happened in the first place.
“This is a huge disappointment to the motorists that have been waiting for years for this road to open to replace the old notorious A1073 and the residents of Eye Green who have been subjected to years of heavy traffic.”
Construction work started in April 2008 under Morgan Est’s Early Contractor Involvement arrangement with the council.
A Lincolnshire Council statement said: “Stability issues have arisen on the embankment approaching Car Dyke Bridge, within the Peterborough section of the scheme.
“The embankment will now require investigation and further work to ensure the long-term durability and safety of this section of the road.
“Geotechnical experts are carrying out tests which will determine the best course of action to stabilise the embankment.
“Until the issue near Car Dyke has been resolved, we are unfortunately unable to open that section of road.”