Byrne Brothers-owned fit-out arm Chorus is understood to have been drafted in to complete the luxury hotel job, which is understood to be nearing completion.
November is now said to be the target opening date, almost a year later than first programmed.
A spokesman for the John Sisk Group said: “John Sisk & Son can confirm that it is no longer working on the Shangri-La fit-out at The Shard.
“Despite our best endeavours, we have not managed to find a way forward with Shangri-La and a decision has been made to end the relationship.”
A subcontractor source said: “Sisk faced a lot of technical challenges on the job and there were design changes throughout which hindered progress.”
Working between floors 34 and 52 of the 1017 feet high Shard has proved challenging because of restricted access and storage space.
The hotly-contested job was won against rivals Chorus, Mivan, Mace and ISG and was a major coup for Sisk as its largest fit-out win in London.
The 13-month long contract got underway in January 2012 . But during the early summer Shangri-La admitted it was taking bookings for a new September opening date. But this has been rescheduled once more.
A statement from the hotel operators said: “Shangri-La Hotel, At The Shard has decided to end their relationship with the present contractors for the fit out.
“A new contractor has been appointed to complete the work. Shangri-La Hotel at The Shard is fully committed to opening and running their latest European hotel.”