The paintings have apparently been taken away for restoration as Se Cathedral is getting ready for the decennial exposition of relics of St Francis Xavier, scheduled next year.
Fr Leonard Correia, Parish Priest of Se Cathedral, the country's largest church located 9 kms away from Panaji, wrote a letter to ASI officials last week claiming that the paintings were removed from various corners and altars without informing him or parishioners.
Fr Correia in his letter to ASI, a copy of which is also marked to Archbishop of Goa and Daman Fr Felipe Neri Ferrao, said that "there is no coordination between ASI and church authorities when such important step is being taken (of taking away the paintings)."
ASI's superintending archaeologist Dr Shivananda Rao was out of station when this reporter tried contact him for his comment on the issue.
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The ASI should have begun the restoration work much earlier as one-and-half year is left for the decennial exposition, considered as one of the biggest religious celebration for Catholics, the parishioner said.
The church is known for its Portuguese-Manueline architectural style. Its construction began in 1562 and completed in 1619.