Netanyahu, in broadcast remarks, said he would tell the envoys, "Israel insists on the separation of forces agreement between us and Syria being honoured, as they were honoured for decades until the civil war in Syria broke out".
In a statement posted to Twitter, the Israel Defense Forces (IDF) said they carried out the evacuation at the request of the United States and European countries.
Those civilians, majority opponents of the Assad regime, remain trapped in the area adjacent to the Israeli border in the assumption Israel will evacuate them as well.
The United Nations says more than 300,000 Syrians have likely been displaced since the government offensive began in southern Syria in June.
However, Syria and its close ally Russian Federation stress that the so-called volunteer group has staged the suspected chemical weapons attack in the town of Douma in Syria's Eastern Ghouta region on April 7.
The US praised Israel and Jordan for facilitating the evacuations and Britain, Canada and Germany for agreeing to give the evacuees new homes.
The official said the rockets were likely aimed at Syrian rebels fighting the government and they eventually landed just one kilometer from the Israeli-controlled Golan Heights.
Jordanian Foreign Ministry spokesman Mohammed al-Kayed says the Syrians will remain in Jordan for three months before moving on to Canada, Britain and Germany.
He said the prospect of regime retaliation has forced the group's members to retreat to safer areas or flee.
The latest deal, agreed on Thursday, saw fighters and civilians evacuated from Quneitra province, which borders the Golan Heights.
"A few days ago President Trump and Canadian Prime Minister Trudeau and others approached me with the request to help extract from Syria hundreds of WhiteHelmets", Netanyahu said in a statement.
Syrian state news agency SANA, citing a foreign ministry official, said the evacuation "exposed the true nature of the organisation known as the White Helmets", calling it a risk to stability and security "because of its terrorist nature". The group is funded in part by the British government.
The Israeli operation was carried out at the request of a number of countries including the United Kingdom, the British foreign secretary, and the global development secretary.
Syria splintered into civil war in 2011 when Assad's regime violently repressed demonstrations against his rule during the pro-democracy Arab spring.
Israel, which technically remains in a state of war with Syria, has been watching the development near its border closely.
Another source familiar with the situation said Islamic State had been able to expand its territory over the last 20 hours by seizing at least 18 villages abandoned by other rebels under the banner of the Free Syrian Army (FSA).
Trump denies report he's frustrated with North Korea
In the lead up to Trump's face-to-face meeting with Kim, the U.S. president showed his masterful deal making skills in action. Secretary of State Mike Pompeo echoed Brook's statement, saying the challenge with North Korea is not over.