Huge blasts rocked the main Greek Cypriot naval base at Zygi in the south of the Mediterranean island early on Monday leaving 12 dead and many injured, a defence ministry spokeswoman said.
Reports from Cyprus confirmed that at least 30 people were injured but final figures are yet to be announced, while it has been reported that the explosions struck among weapons seized from an Iranian shipment in 2009.
The official CNA news agency said five fire-fighters, four members of the Greek Cypriot National Guard and two sailors were killed, citing military sources.
A defence ministry spokesman interviewed by public radio confirmed that there were deaths but declined to give a figure.
Witnesses told the radio of a scene of devastation in the adjacent fishing village whose seafront restaurants are popular with the many tourists who frequent the resort island.
Cars, houses and restaurants alike suffered massive damage from the force of the blasts, the witnesses said and Commerce Minister Antonis Paschalides told the radio it was a "tragedy of Biblical dimensions."
The radio said that the fire brigade were called to a blaze near the base at 4:24 am (0124 GMT) and that the explosions followed at 5:50 am (0250 GMT).
As the cause of the blasts is for now still unknown, state media quoted Greek Cypriot National Guard chief Petros Tsaliklides as saying that it struck among containers of Iranian munitions seized from Cypriot-flagged vessel M/V Monchegorsk.
The vessel was intercepted in the eastern Mediterranean en route to Syria in January 2009 and, after repeated searches, its cargo was eventually seized.
A UN Security Council panel concluded in March that year that the shipment was in clear violation of an arms embargo against Iran adopted as part of UN sanctions over Tehran's controversial nuclear programme and the seized weapons were put into storage.
"There were 98 containers of gunpowder. Two of them (caught) fire and huge explosions occurred," a police spokesman told the state CNA news agency.
There were reports of extensive disruption to traffic in the Monday morning rush hour as a number of major roads were closed.
The Iranian weapons were seized under a 2007 sanctions resolution adopted by the Security Council, which requires that "Iran shall not supply, sell or transfer from its territory any arms and related materiel, and that all states shall prohibit the procurement of such items from Iran."
According to Israeli media, officials were convinced the Monchegorsk was carrying Iranian arms destined for the Hamas-ruled Gaza Strip and the Cypriot authorities decided to detain the vessel following requests from both Israel and the United States.
Israel has long accused Iran of arming Islamists in Gaza, a charge Tehran denies even though it says it acknowledges it offers moral support to Hamas.
Iran reacted furiously to the interception of the cargo and strongly denied accusations that the weapons were intended for either Hamas or the Lebanese Shiite militant group Hezbollah.