North Korea accused Mexico on Wednesday of illegally detaining the Mu Du Bong, a 6,700-tonne North Korean cargo ship.
Mexico's foreign ministry said on Thursday it is only holding the ship to comply with United Nations rules.
The freighter was sailing from Havana, when it hit a reef about 13 km from the Mexican port of Tuxpan in July last year.
North Korea had paid an undisclosed sum to Mexico for damages, hoping the ship and its crew of 33 would be released.
But the impounded ship connected was to Ocean Maritime Management, a firm blacklisted by the United Nations Security council after another of its ships, the Chong Chong Gang, was found transporting arms from Cuba in 2013. The ship will remain at the Tuxpan port until an investigation is concluded.
North Korea has warned that it would take "necessary measures" for the vessel to be released.
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