Jordan officially closed its border with Syria last year, Xinhua reported.
"Those stranded at the borders came from areas in the north of Syria which are controlled by IS," Jordan's Minister of State Mohammad Momani said on Sunday.
However, it receives Syrian refugees daily through several areas from those borders.
Momani said there were around 16,000 Syrian asylum seekers located in no-man's land, in the north eastern part of Jordan, along the border with Syria.
Jordan has acquired intelligence that among the asylum seekers were IS militant group members and supporters, he added.
"Jordan will regulate this issue with security measures in mind," said the minister, a few days after Jordan decided not to allow Syrian asylum seekers into the country.
"Jordan's borders are open to refugees and around 50-100 enter Jordan daily, with a focus on children and the elderly," said the minister.
Jordan then allowed the establishment of a refugee camp in no-man's land serviced by international relief agencies.
He added that Jordan provides services to those refugees as well.
According to official figures, there are currently around 1.5 million Syrians refugees in Jordan.