The Jordanians have said no twice to the permission but I'm guessing that the Israelis feel they have done enough to cover themselves now with the Jordanian government.
The story comes from Israel National News.
Report: Israel Asked Jordan for OK to Bomb Syrian WMDs
Israel has consulted with Jordan twice over the issue of Syria's chemical weapons arsenal, according to a report published Monday by The Atlantic, both times with plans to take out multiple sites. According to intelligence officials in two countries quoted by correspondent Jeff Goldberg, "Israel has been seeking Jordan's 'permission' to bomb these sites, but the Jordanians have so far declined" to agree.
As Goldberg pointed out, Israel does not need Jordan's approval to bomb an arsenal that could prove to be an existential threat to its citizens. A nuclear reactor built by North Korea in Syria in 2007 was quietly eliminated by the IAF. But according to the report, Israel is concerned about the possible repercussions for Jordan of an attack on Syrian chemical weapons storage facilities, because a number of the sites are apparently close to the Syrian-Jordanian border.
"The Jordanians have to be very careful about provoking the regime and they assume the Syrians would suspect Jordanian complicity in an Israeli attack,” Goldberg quoted the source as saying. "You know the Israelis – sometimes they want to bomb right away. But they were told that from the Jordanian perspective, the time was not right.”
Allegedly the contacts between Israel and Jordan over the issue were made through Mossad envoys sent by Prime Minister Binyamin Netanyahu's office during the past two months. Goldberg received no reply from Israel's embassy in Washington to his request for comment or verification of the information.
A diplomatic source in the Middle East told media Monday evening that Syrian Foreign Ministry spokesman Jihad Makdissi has defected. The source said that Makdissi had reportedly been thrown out of the government for issuing statements that were opposed to the position of the Syrian regime.
Most recently the Foreign Ministry claimed that the Syrian government would not use chemical weapons against its own people. In a statement broadcast on government-run national television earlier today (Monday), the country's foreign ministry assured the international community President Bashar al-Assad would not approve such a measure.