People smugglers fired several warning shots at vessels during a search and rescue operation on 13 April, EU border agency Frontex reported.
The international agency said shots were fired in an attempt to recover a wooden boat used for transporting migrants to Italy.
The incident occurred 60 nautical miles from the Libyan coast after an Italian tugboat and Icelandic Coast Guard vessel Tyr deployed by Frontex rescued immigrants from a vessel.
They were later approached by a speedboat that, after firing warning shots, sped away with the empty migrant boat.
"Last Monday one of the vessels deployed by Frontex to Italy within the framework of operation Triton witnessed warning shots fired by the smugglers who were attempting to take the boat originally carrying the migrants back to Libya," said spokesperson Izabella Cooper.
"This is the clear sign that the smugglers in Libya are running out of boats, and therefore they are determined to do anything including shooting their guns in order to do that, in order to keep their boats and possibly be able to reuse them for further smuggling operations."
This is the second time in 2015 that armed smugglers took back a vessel used to transport migrants following a rescue operation in the Central Mediterranean, Frontex said.
"This year, since the beginning of January, we've registered about 18,000 migrants departing from Libya. These are very concerning, very high numbers. Most of them require search and rescue because smugglers put them on tiny, flimsy, unseaworthy boats. Sometimes these are rubber dinghies which are 10 to12m long carrying 130, 140 migrants."
Nearly 6,000 migrants have been rescued within the past four days with more boats expected. Save the Children said about 400 migrants died in an attempt to reach Italy from Libya when their boat capsized, according to survivors interviewed at a port in Reggio Calabria.
The charity said the boat, carrying about 550 migrants in total, flipped about 24 hours after leaving the Libyan coast, according to some of the 150 survivors who were rescued.