Cono Galipo said in a radio interview that the migrants seen lining up naked had in fact stripped down because they were "impatient" as they awaited their disinfection shower and had "clearly staged the images seen".
Footage broadcast by Rai on Monday shows people being hosed down in what was described as an attempt to combat scabies, said to have been picked up after migrants arrived on the island.
Lampedusa Mayor Giusy Nicolini said the images reminded her of a "concentration camp", while Laura Boldrini, president of the Chamber of Deputies, said the scene was “shameful for a civil country”.
The EU's home affairs commissioner, Cecilia Malmström, released a statement on Monday describing the footage as "appalling and unacceptable" and threatened.
But Galipo defended the centre and said "it should all be contextualized".
"We had just had three landings in which the risk of scabies was very high.
"Usually when there are a few people we do the treatment in the clinic but there were 104 people and there was no other space free," he said.
The island's 381-bed facility is often too full and many migrants have been forced to stay in unsanitary conditions and sleep out in the open, awaiting transfer to other migrant centres in the rest of Italy.
Tens of thousands of migrants have landed in Italy this year, 14,000 of which have transited through Lampedusa.