The seizure took place on Friday after the marines detected through intelligence work a small boat in the Pacific waters, some 139 kilometers northeast from Port Chiapas, located near the Mexican border with Guatemala.
An aircraft, a helicopter and two oceanic patrol vessels were used in the operation, according to the report.
A video released by the ministry showed marines rope-landing in the boat from a helicopter.
The authorities said that the smugglers threw 38 bags of cocaine into the sea, however, the marines were able to retrieve them.
Seven people were arrested in connection with the case.
Friday's seizure was the second operation of its kind in the south of Mexico in less than a week.
On Monday, the Army intercepted an aircraft carrying 450 kilograms of cocaine in a coastal city in Chiapas.
The cocaine that Mexico seizes on its territory often comes from South American cartels, according to the ministry.