Mr Duterte ordered the ban after reports emerged about the deaths of several Filipina women in the Gulf state, his spokesman Harry Roque said. The Philippine president himself has been accused of human rights violations in the past.
"In line with his presidential pronouncement, Labour Secretary Silvestre Bello has ordered the suspension of the deployment of workers to Kuwait," Mr Roque told reporters.
"There is really excessive suffering over there," Mr Roque said, adding that the ban was "long overdue".
An estimated 10 million Filipinos work overseas and the money they send home is a major pillar of the Philippine economy.
It was not immediately clear how long the ban, which does not affect workers already in Kuwait, would last.
In his speech before overseas workers on Thursday, Mr Duterte said he would urge the Kuwaiti government to act against the abuses.
"I do not want a quarrel with Kuwait. I respect their leaders, but they have to do something about this," he added.
Spokesmen for the Kuwaiti embassy in Manila could not be reached for comment.
Kuwait has faced criticism in the past over its "kafala" system for foreign workers which has been likened to a form of bonded labour or even slavery.
The kafala system prevents workers from moving to a new job before their contracts end without their boss's consent, resulting in a wide range of abuses.
The Gulf state is a major destination for migrant workers with the Kuwaiti government estimating that more than 170,000 Philippine nationals live there. Other groups have far higher estimates.