Local sources told AFP the employees, all Yemeni citizens, were taken in a Thursday raid over accusations they had accepted and distributed aid from a Saudi-led coalition, which has been battling the Huthi rebels since March 2015.
The 12 employees were taken hostage from the aid group's offices in the Hali district of rebel-held Hodeida late last week, Local Affairs Minister Abdul Raqib Fattah said in a statement carried by the pro-government sabanew.net news website.
Yemen's conflict pits a Saudi-led Arab coalition supportive of President Abedrabbo Mansour Hadi against Iran-backed Huthis, who currently control the Red Sea port of Hodeida along with the capital Sanaa and large parts of northern Yemen.
Monday's news comes amid a push by forces loyal to Hadi, backed by the Arab coalition, to close in on Hodeida, located on Yemen's western coast.
Forces loyal to the government took full control of Mokha, south of Hodeida, earlier in February as part of a major offensive to oust the Huthis and their allies from Yemen's southwestern coast.
Yemen's conflict escalated in March 2015 when the Saudi-led coalition began air strikes to help forces loyal to Hadi to take large parts of the country back from the rebels.
More than 7,400 people have been killed and nearly 40,000 injured in two years of fighting in Yemen, according to the World Health Organisation.
UN humanitarian coordinator for Yemen James McGoldrick in January said more than 10,000 civilians had been killed since 2015.
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