Maroni said an investigation has begun, adding he believed Libya mistook the trawler for a boat carrying illegal immigrants, Italian news agency ANSA reported.
"What occurred the other (Sunday) evening should not have taken place and Libya has apologized," Maroni said.
None of the 10-member crew of the Ariete was injured.
The minister said the boat was one of six Italy gave Libya under a 2007 agreement.
"While it is true that Italian military personnel were on board, they were only offering technical assistance and were not part of the crew," he said.
Gaspare Marrone, the Ariete's captain, said that before the Libyan boat opened fire he received a radio warning that said -- "Stop or we will fire."
Marrone said the incident occurred in the Gulf of Sirte, about 30 nautical miles off Libya. Italy considers these waters international, but Libya maintains it has jurisdiction and regularly repels straying vessels, ANSA said.
Italian Foreign Minister Franco Frattin said the incident was "serious," but "does not change relations between Italy and Libya."