The head of the far-right League ordered the country's regional prefects to draw up “a report on the presence of Roma, Sinti and Caminanti” within two weeks, the interior ministry said in a statement.
“The aim is to verify the presence of illegal camps to draw up an eviction plan,” it said.
The Roma, Sinti and Caminanti are traditionally nomadic ethnic groups who have lived in Europe for centuries.
The Sinti are traditionally from west and central Europe, while Roma have their origins in the east and southeast of the continent. The Caminanti are believed to have their origins in the Norman occupation of Sicily.
The pro-Roma group Associazione 21 Luglio said Tuesday it was “deeply worried” by Salvini's order.
It slammed “a measure which clearly discriminates against these communities, since it does not affect, for example, formal or informal settlements inhabited by persons not belonging to these ethnic groups”.
Some 25,000 Roma, Sinti and Caminanti live in conditions of “housing segregation”, according to the association, accusing the government of maintaining “ethnic ghettos”.
About 15,000 members of the three groups reside in 127 formal settlements in Italy, often in the suburbs of large cities, according to the group.
The rest live instead in informal settlements, some of which are made up of just two to three families.
There are about 300 such informal settlements in Rome, the Associazione 21 Luglio told AFP.
Threats against the Roma and Sinti have increased under Salvini, who sparked controversy last year with his call for a new census of Roma, and for all non-Italians among them to be expelled from the country.
Salvini has also barred Italy's ports to charity vessels rescuing migrants at sea.
The Council of Europe estimates there are between 120,000 and 180,000 Roma, Sinti and Caminanti in Italy — one of the lowest concentrations in Europe.
Over half are Italian citizens with regular jobs and homes, but hate crimes against their less fortunate peers are rife.