An investigation by a European rights group published on Monday found that Israeli-made Pegasus spyware was used to hack the phones of staff of Palestinian civil society groups targeted by Israel.
The revelations by Frontline Defenders - backed up by Amnesty International and the University of Toronto's Citizen Lab - mark the latest development in the widening controversy surrounding six prominent Palestinian groups designated as "terrorist" organisations by Israel's defence ministry last month.
Pegasus - made by the NSO company that was put on a US blacklist last week - turns phones into pocket spying devices, giving users total access to the target's phone contents without them knowing.
Israel insists the designated Palestinian groups work in collaboration with the Popular Front for the Liberation of Palestine (PFLP), a Marxist group labelled a terrorist organisation by many Western states.
There has been widespread criticism of the terrorist designation slapped on the groups Addameer, Al-Haq, Bisan Center for Research and Development, Defense for Children International – Palestine (DCI-P), the Union of Agricultural Work Committees (UAWC), and the Union of Palestinian Women's Committees (UPWC).
According to the Frontline Defenders investigation, six devices used by employees of the targeted groups "were hacked with NSO Group's Pegasus spyware", including US citizen Ubai al-Aboudi, head of the Bisan Center, and French national Salah Hammouri, a researcher at Adameer.
Amnesty International's Security Lab and Citizen Lab upheld those findings.
Israeli officials declined to comment on allegations that Pegasus was used against the Palestinian groups.
Speaking Saturday in response to a question about NSO's blacklisting by Washington, Israel Foreign Minister Yair Lapid underscored it was a "private company... not a governmental project".
Israel's rules governing "cyber-warfare" were among the world's strictest, he said.
But Israel has pushed back against charges that its evidence justifying the terrorism designations was lacking.
Briefing journalists on Monday, an Israeli security-diplomatic source said investigations had yielded an "excellent file" of evidence linking the groups to the PFLP.
A logo adorns a wall on a branch of the Israeli NSO Group company, near the southern Israeli town of Sapir Source: AP
The briefing came after several media outlets gained access to a 74-page Israeli evidence dossier compiled in May.
The dossier was first obtained by Israeli outlets +972 Magazine and Local Call.
It did not appear to contain clear evidence connecting the groups to the PFLP, and was based largely on unsubstantiated statements.
But the Israeli official said Monday: "The assumption that all we have is the dossier from May is simply wrong.
"Source after source indicates that these are the top of the PFLP," the official said regarding the leadership of the six groups.
The organisations have received European donor funding and EU officials have raised concern about the designations.
Irish Foreign Minister Simon Coveney told the Jerusalem Post newspaper last week that the EU had "not gotten any credible evidence linking the NGOs to terrorism".
The Israeli official said different international officials had received different levels of intelligence so far, but that broadly EU governments "understand well that the organisations are not clean".
"We have begun another round of presenting information to the Europeans," he said, adding that Israel believed EU donors were victims of a "smoke-screen" and did not know where their taxpayer money was going.
"We are not accusing the Europeans of funding terror," the official said.
The defence ministry has said the groups had hosted PFLP meetings, employed "convicted terrorists" and operated as a "lifeline" for the PFLP through "fundraising, money laundering and recruitment of activists".
