The firm started the job in March 2010 with a revamp of the Greenwich foot tunnels due to be completed in 12 months.
But the project suffered cost and time overruns which resulted in Dean & Dyball leaving the unfinished site in December 2011.
The council took direct control of the job but local residents are unhappy about the condition of the tunnels and the fact that one set of lifts is still not working.
Council chiefs have consulted lawyers as they pursue a claim against Dean & Dyball .
A new contractor is also needed for a four month work programme to install lifts at the Woolwich foot tunnel, re-roof the Greenwich north and both Woolwich rotunda and deep clean the tunnels.
A council statement said: “The Royal Borough of Greenwich shares the frustration of pedestrians and cyclists over the time taken to complete this project and, whilst both tunnels remain open, we apologise for the unacceptable delays to this work.
“The council is now in the process of procuring a new contractor to complete the project and is taking legal advice from a firm of specialist construction lawyers on the best route to recover the additional costs from the contractors.”
A Balfour Beatty spokesperson said: “Dean & Dyball Civil Engineering is in ongoing negotiations with its customer, Royal Borough of Greenwich, regarding this matter and as such it would be inappropriate to comment further at this time.”