"We'll go ahead with the census and with all the other measures," Roberto Maroni was quoted by Corriere della Sera as saying.
Maroni, speaking to lawmakers this week, explained that his plan was "to fingerprint all (Roma), including children, to avoid phenomena such as begging."
The center-left opposition was quick to attack Maroni, calling the proposal unacceptable and uncivilized. "It is an act of racism," centrist leader Pier Ferdinando Casini said Saturday.
In recent weeks, Italian officials have spoken of a "Roma emergency" in big cities, linking crime to the Roma, also called Gypsies.
In Naples, camps had to be evacuated after attackers set huts on fire and angry residents in neighboring areas protested against the alleged attempt by a Gypsy woman to kidnap a baby. Authorities in Rome raided a camp to check for proper papers.
"I have been elected to solve the problem of security and I will do that without being affected by groundless controversy," said Maroni, a senior member of the government and a leading official of the anti-immigrant Northern League party.
Maroni said the measure is not discriminatory and insisted it is for the good of "many children who live in appalling conditions," according to Corriere.
"I must be able to know who is in Italy, where they live, what they do, what they will do in coming months," Maroni was quoted as saying. "It's no secret that children who are exploited and commit crimes are moved from one city to the next to escape checks."
Maroni has also said that members of the Red Cross would be present to ensure that the human rights of the Roma are respected. He said that Roma parents who send their children to beg on the streets rather than to school would lose custody of their children.
The Italian chapter of the U.N. Children's Fund expressed "surprise and grave concern" over the proposal.
"One cannot - in order to 'protect' children - violate their fundamental rights. We cannot turn victims into criminals," the president of UNICEF Italia Vincenzo Spadafora said in a statement Saturday.
Outside of Italy, Council of Europe Secretary-General Terry Davis said that "this proposal invites historical analogies which are so obvious that they do not even have to be spelled out."
"While I believe that Italian democracy and its institutions are mature enough to prevent any such ideas becoming laws, I am nevertheless concerned that a senior member of the government of one of Council of Europe member states is reported to have made such a proposal."