Israel is arming submarines supplied and largely financed by Germany with nuclear-tipped cruise missiles, influential German news weekly Der Spiegel reports in its issue to be published on Monday.
The magazine said in a cover story that Berlin had until now denied any knowledge that German submarines were being used as part of an Israeli atomic arsenal.
But former high-ranking officials of the German defence ministry told Der Spiegel that the government always assumed Israel was putting nuclear warheads on the Dolphin-class vessels.
The article, based on a months-long probe, cited files from the foreign ministry in Berlin indicating the West German state was aware of the practice as early as 1961.
In Israel, foreign ministry spokesman Yigal Palmor said only: "I can confirm that we have German submarines. It's no secret.
"As for the rest, I am not in a position to talk about their capacity," he told AFP.
Israel is the Middle East's sole if undeclared nuclear-armed power.
Germany has already supplied Israel with three of the submarines in question, footing most of the bill, and another three are to be delivered by 2017 under a recently signed contract.
Meanwhile Israel is weighing whether to order three more, according to the report.
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"The Germans can be proud to have ensured the existence of the state of Israel for several years to come," Israeli Defence Minister Ehud Barak was quoted by Der Spiegel as saying.
The opposition Social Democrat Party called Sunday on Chancellor Angela Merkel's government for an explanation.
"The federal government must provide information so that we know if the submarines delivered by Germany can be potentially equipped with nuclear warheads," party spokesman Rolf Muetzenich told Der Spiegel.
Merkel's spokesman Steffen Seibert said all submarines had been delivered unarmed.
"The federal government will not speculate on subsequent arming," he said.
The report said Germany hoped to see Israeli concessions on settlements on Palestinian land and approval for the completion of a sewage treatment plant in the Gaza Strip in exchange for the assistance.
Israel sees its existence under threat if its arch-foe Iran goes nuclear. Like the United States, it has refused to rule out bombing Iranian nuclear sites.
Germany, bearing the historical guilt of the Holocaust, is Israel's closest ally in Europe.
But it has sharply criticised Prime Minister Benjamin Netanyahu's pro-settlement policies in the West Bank and annexed east Jerusalem as undermining peace efforts with the Palestinians.
Tensions between Germany and Israel flared in April when Nobel prize-winning German author Gunter Grass published an inflammatory poem warning that a nuclear-armed Israel "could wipe out the Iranian people (with a) first strike."