In another example of the group's brutality, a video posted on YouTube this week apparently shows Isis fighters leading stripped Syrian soldiers into the desert and shooting them in a mass execution.
An Isis fighter confirmed the video's authenticity to Reuters, saying: "Yes, we have executed them all."
A statement posted online and circulated on Twitter by supporters of Isis claimed the extremists killed "about 200" government prisoners captured near the Tabqa air base.
The Syrian Observatory for Human Rights said the soldiers were captured when they attempted to flee the fallen air base in Raqqa. It put the death toll at 120.
According to the UN refugee agency, many of the new arrivals in Jordan come from the northern province of Aleppo and the northeastern region of Raqqa, a stronghold of the group. An independent UN commission says the group is systematically carrying out widespread bombings, beheadings and mass killings that amount to crimes against humanity in both areas.
The commission investigating potential war crimes in Syria said on Thursday that the Syrian Government of President Bashar al-Assad likely used chlorine gas to attack civilians, who are bearing the brunt of a civil war that has killed more than 190,000 people and destabilised the region.
The massive numbers of Syrians fleeing the civil war has stretched the resources of neighbouring countries and raised fears of violence spreading in the region.
The UN estimates there are nearly 35,000 people awaiting registration as refugees, and hundreds of thousands who are not registered.
International Rescue Committee President David Miliband said the Syrian refugee crisis represents "three million indictments of government brutality, opposition violence and international failure".
"This appalling milestone needs to generate action as well as anger," he said, calling for more aid to Syria's overburdened neighbours and for civilians still in the country.
The refugee agency and other aid groups say an increasing number of families are arriving in other countries in shockingly poor condition, exhausted and scared and with almost no financial savings left after having been on the run for a year or more.
In eastern Jordan, for example, the agency says refugees crossing the desert are forced to pay smugglers US$100 ($119) per person or more to be taken to safety. Lebanon hosts 1.14 million Syrian refugees, the single highest concentration. Turkey has 815,000 and Jordan has 608,000.
AP