According to information on the Jordanian military's website, an unspecified number of people were wounded while others fled back into Syria.
The military official added that more than two million pills of narcotics were also seized.
Jordan regularly expresses fears of terrorists infiltrating refugee groups to justify curbs on Syrian refugees massing on the border, estimating their number at 16,000.
Amman has been allowing just a few dozen Syrians to cross the frontier daily amid stringent identity checks.
According to UN figures, Jordan hosts upwards of 600,000 of the more than four million Syrians who have fled their native country since the civil war erupted there in 2011.
Jordanian government figures put the number of Syrians to have entered the country after fleeing the conflict at more than 1.4 million, AFP Reports.
Meanwhile Jordanian Minister of State for Media Affairs and Communications Mohammad Momani says supporters of Daesh militant group, who fled terror group occupied territories are among Syrian refugees in the camps near the Syrian-Jordanian border.
On Sunday, Momani held a press conference regarding country's policy toward accepting refugees. He was asked a question about the future of some 12,000 Syrian refugees from camps across the Syrian-Jordanian border.
“Jordan maintains its open door policy…but we do have security concerns, and this group specifically came from the far northeast of Syria, areas that are controlled by Daesh,” Momani said on Sunday, as quoted by The Jordan Times newspaper, adding that there were Daesh supporters and even members of the group among the refugees.
He added that Jordan took the issue of its security very seriously.
Syria has been engulfed in a civil war since 2011, with syria fighting against terrorist groups such as the Daesh, which is prohibited by many countries, including Russia and the United States.
The internal conflict have already made more than 4,6 million refugees flee Syria to neighboring countries, including more than 630,000 of them to Jordan, according to UN data.