The Iuventa, operated by the Jugend Rettet organisation, was "preventatively" impounded on the Italian island of Lampedusa on the orders of a prosecutor based in Trapani, Sicily, the state police force said in a statement.
"Enquiries begun in October 2016, and conducted with the use of sophisticated techniques and investigative technology, have produced circumstantial evidence of the motorboat Iuventa being used for activities facilitating illegal immigration," the statement said.
More details were to be provided at an afternoon press conference.
The impounding of the Iuventa came as Italy began enforcing a controversial code of conduct for charity boats rescuing migrants in the Mediterranean.
Jugend Rette was among six of nine NGO's operating search-and-rescue activities in waters off Libya to reject the new rules. Italian authorities say they are necessary to ensure the boats are not effectively encouraging migrants to embark on the perilous crossing.
The NGOs have particularly objected to a requirement to allow an Italian police official to travel on each boat and a ban on moving rescued migrants from one aid vessel to another while still at sea, which they say could result in avoidable deaths.
Some 600,000 mostly African migrants have arrived in Italy from Libya since the start of 2014, putting the country's reception facilities under strain and the centre-left government under pressure over the crisis.
Just over a third of those rescued this year have been saved by NGO boats, up from around a quarter last year.