The ship had sought permission from authorities only after nearing the port, defence secretary Dr. Karunasena Hettiarachchi has told BBC Sandeshaya.
The ship has breached several regulations, about which two reports have been submitted.
Police are tasked with initiating legal action, while the Navy is conducting a separate inquiry, he said.
Avant Garde still under probe
Hettiarachchi also said the presidential commission is carrying out several investigations with regard to Avant Garde.
Clarifying a claim by the attorney general that there was no evidence to prosecute Avant Garde, he said the issues investigated might not have pointed to any reasons for prosecution.
However, other investigations are ongoing against Avant Garde, whose ship at Galle port had 813 firearms and more than 200,000 rounds of ammunition, he said.
Guidance or order is expected from the presidential commission with regard to investigations into the agreement between Avant Garde and Rakna Lanka, said the defence secretary.