The spokesman confirmed reports the boat was infested with rats and lice and had to be professionally fumigated.
"Since taking control of the vessel, part of the monthly maintenance costs has been pest detection and control," he said.
The ministry would apply to the courts for recovery of all expenditure associated with holding and maintaining the vessel, he said.
A ministry application to the Christchurch District Court for the vessel to be sold pursuant to the Search and Surveillance Act 2012 had yet to be decided by the courts.
Witnesses had also provided evidence.
A conclusion to the defended hearing in relation to charges against officers aboard Melilla 201 was scheduled for June.
The charges relate to two fishing trips during 2011, the same year the vessel and its sister ship, Melilla 203 - which is also berthed in Dunedin - became embroiled in claims from their Indonesian crews of unpaid wages.
The trawlers are owned by Taejin Fisheries, which is based in Pusan, South Korea.