Police were immediately called to the site in Waterford, where they determined the skulls and bones were too old to be of forensic interest, The Irish Times reported.
"We were satisfied that no crime had been committed so it's nothing to do with us now -- the remains definitely weren't put in there yesterday," said Gardai Sgt. Larry Langton.
Jack Burchill, a Waterford historian, said the area where Egan's, a historic pub, stood until recently was once a Dominican abbey. The abbey, like many others in Ireland and England, was shut down by King Henry VIII when he rejected the authority of the pope in 1540.
The bones probably date from the abbey era, Burchill said. Local people may also have continued to use the site as a burial ground after the abbey was closed.
Dave Pollock, supervisor of the excavation, said workers at the site are used to dealing with bits of Waterford's past in a city founded in the 10th century. The expanded Penneys store will include a section of the old city wall.