The energy company warned in November that water levels in the reservoir were higher than was expected so early in the development, which began production in August 2013.
Encana says it plans to resume production at Deep Panuke closer towards winter, when demand for natural gas is the greatest.
The gas wells, which are located about 250 kilometres east of Halifax on the Scotian Shelf, have faced a series of problems in recent years.
Operations at Deep Panuke were shut down in August 2014 and in January 2013 due to electrical fires.
Natural gas from Deep Panuke is processed offshore and transported via subsea pipeline to Goldboro, N.S., where it connects with the Maritimes and Northeast Pipeline.