Aluf Benn of the Israeli newspaper Haaretz reported on Thursday that "a highly classified problem" between Russian and Israel was the real reason for the emergency meeting convened by Israeli Prime Minister Ariel Sharon earlier this week.
The meeting was attended by Israel's Foreign Minister Silvan Shalom, Defence Minister Shaul Mofaz and intelligence officials.
Then the Israeli media was told that the meeting was precipitated by concern over recent "anti-Semitic statements" allegedly made by President Vladimir Putin.
However, Haaretz's government sources said this rationale was "only partial and tendentious" and was aimed at concealing the real reason for the crisis which Sharon insisted be kept secret.
Russian President Vladimir
A spokesperson for the Israeli foreign ministry acknowledged that there is a "problem" between the two countries, but refused to give any details.
Similarly the press attaché at the Russian embassy in Tel Aviv refused to "confirm or deny" the Ha'aretz report.
He told Aljazeera.net he was in no position to comment on the story.
A high-ranking European diplomat based in Jerusalem told Aljazeera.net that the reported crisis might have something to do with espionage.
"It is no secret that the Mossad has been making efforts to disrupt Russia's supplies of nuclear materials to Iran"
high-ranking EU diplomat based in Jerusalem
"It is no secret that the Mossad has been making efforts to disrupt Russia's supplies of nuclear materials to Iran," the EU diplomat, who spoke on the condition of anonymity, said.
Yossi Alpher, a noted Israeli political analyst, ruled out rumours that the reported crisis was probably connected with secret Jewish Agency activities aimed at prompting more Russian Jews to emigrate to Israel.
He also said that Israel would never seek to upset Russian by doing "foolish things" like supplying arms to Chechen rebels.