Developers who built the council HQ building are in breach of a planning condition for not completing the archaeological work.
Cheshire West and Chester Council has issued a breach of condition notice against Swansea-based Liberty Properties Ltd for failing to produce a full report for publication in an academic journal and failing to deposit the archive at the Grosvenor Museum within three years of completion of the fieldwork.
Archaeologists carried out the dig prior to construction of the council offices, luxury apartments and Abode hotel in the largest excavation to have taken place in Chester in more than 30 years.
City archaeologist Mike Morris said the excavation would transform the view of the Roman town and medieval nunnery.
The foundations for at least one large Roman town house were discovered including an undisturbed mosaic floor – the first to be found in Chester since 1909.
This find, along with pieces of painted wall plaster, suggested it was a high status building, the home of a wealthy merchant or Roman official.
Traces of the medieval Benedictine nunnery and cemetery were also revealed along with more than 100 skeletons. This was the earliest of the religious houses to be founded in Chester in the 12th century. A beautiful gold ring dating from the time of the nunnery was also found.
The company is warned that it faces prosecution in the magistrates court and a fine of up to ï¿½1,000 if fails to complete the post-excavation programme within two years of the notice being issued.