The state capital with more than 200,000 residents is suffering from the unfortunate timing of heavy fertilization by local farmers and prevailing winds that are blowing over the city.
Pope Benedict XVI is due to visit the city in September and to give a service at the city's cathedral.
A spokeswoman for the city said that the recent break in rainy weather gave farmers around the city the chance to fertilise their fields with dung. Many have done so, in abundance, particularly to the west of the city where pastoral areas are concentrated.
But with a subsequent westerly wind blowing, the overwhelming stench of the manure has wafted over the city. The smell is particularly strong in the inner city, which is renowned for its intact medieval old town.
The spokeswoman said this was of course unpleasant especially for tourists and described the cloud as an unfortunate and temporary incident.