The complaints included rape, maltreatment and non-payment of wages, she said.
"I received an order [from Arturo Brion, the Labour secretary] to stop the deployment of [workers] to Jordan and this is because of the growing number of Filipinos in distress," Baldoz told a press conference.
The ban is only for newly hired workers and does not apply to those returning to employers of "good-standing", she added.
Away from home
Baldoz also said the Philippine government was arranging the possible repatriation of many of these workers.
In Jordan, Majed al-Habashneh, secretary-general of the labour ministry, said the ministry was not officially informed of the action being taken, the Associated Press news agency reported.
He said the ministry was in contact with the Philippine Embassy via joint committees that deal with worker problems in Jordan.
There are 16,274 Filipinos currently working in Jordan.
Eight million Filipinos, about 10 per cent of the Philippines' population, work overseas and from January to November last year, Filipino workers sent home over $13bn.
Aside from Jordan, the Philippines has also banned the deployment of workers to Nigeria, Lebanon, Iraq and Afghanistan.