The ministry said Friday that the SAIPEM 10000 rig belonging to the Eni-Kogas consortium drilled to a depth of 5,800 meters (19,000 feet) without success.
The ministry said new drilling will begin elsewhere inside an area, or block, where Cyprus has licensed the consortium to search for fossil fuels.
The consortium had identified six potential gas fields inside the block.
Cyprus has also licensed France's Total and U.S. firm Noble Energy to search for offshore gas.
Noble and Israel's Delek and Avner are partners in a Cypriot gas field that's estimated to contain between 3.6 trillion and 6 trillion cubic feet of gas.