The agency, quoting government spokesman Mohamed Momani, said the estimated 50,000 refugees were massed around the desert border posts of Hadalat and Rokban.
In January, Jordan had estimated their number of 16,000 and appealed for assistance from international relief agencies.
"Because of the security situation, Jordan has to tightly control the Syrian refugees before allowing them to enter, giving priority to the elderly, women and children," it said.
Momani said 75 relief workers paid daily visits to the refugee camps under the supervision of different aid organisations.
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UN High Commissioner for Refugees (UNHCR) Filippo Grandi said at the start of the year that he fully understands the security concerns which have led Jordan to limit the flow of refugees entering from war-torn Syria.
Jordan has insisted it must screen newcomers to ensure they are genuine refugees and not jihadists seeking to infiltrate the country.
The kingdom is now only allowing in a few dozen refugees each day after the screening process.
Jordan already hosts more than 630,000 Syrian refugees, according to the UNHCR.
Its government gives a much higher estimate of 1.4 million refugees, because many of them are unregistered.