The move was part of a US plan to close the facility.
According to Uruguayan media, the ex-prisoners failed to adapt to their new life in the Latin American country, did not accept job offers and quit their Spanish studies.
Opinion polls indicate that most Uruguayans rejected the decision taken by outgoing President Jose Mujica.
Foreign Minister Rodolfo Nin Novoa said Uruguay would stop taking refugees from the Syrian conflict.
Decisions on accepting new refugees from Syria will be put on hold "just until the end of the year," Nin Novoa said.
Uruguay has faced "cultural and infrastructure" problems to deal with the Syrian families, he explained.
Local media have reported several alleged incidents of domestic violence involving Syrian refugees.