The video, which aired Monday on state-run RAI television, showed a dozen male migrants who lined up in a warehouse, then stripped to be hosed down with a solution to treat scabies.
One of the migrants told RAI that men and women had been disinfected this way a few days ago.
The video was particularly troubling since the government had promised to improve conditions at the overcrowded Lampedusa centre after more than 360 would-be refugees drowned offshore in October, a tragedy that cast worldwide attention on the plight of migrants trying to reach Europe and the conditions they find when they reach land.
Laura Boldrini, president of the lower Chamber of Deputies and a former spokeswoman for the UN refugee agency, called the treatment "degrading and unworthy of a civilised country."
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Premier Enrico Letta promised an investigation and said those responsible would be punished.
The video aired on the eve of the World Day of Migrants, and human rights groups were already geared up to denounce Italy for the conditions at its overcrowded holding centres.
The UN High Commissioner for Refugees said the conditions in Lampedusa, in particular, were unacceptable and demanded the immediate transfer of would-be refugees to other centres on the Italian mainland where their asylum claims can be processed. The Lampedusa centre is designed to hold some 250 people but often four or five times that many people are housed there.
UNHCR denounced the continued detention on Lampedusa of 26 Syrians and Eritreans, including some survivors of the October 3 tragedy. A judge has designated them as witnesses to the capsizing, which only 155 people survived.
In the days after the tragedy, European Commission President Jose Manuel Barroso had travelled to the island and announced that Italy would get 30 million euros more to help welcome and settle refugees to avoid the overcrowding that often occurs at Lampedusa, which is the destination of choice for smuggling operations from Libya and Tunisia.
Some 40,244 migrants arrived in Italy between January and November, one-fifth of them minors, Save the Children reported.