The two attacks happened in the same place in Baghdad in the past two days, a spokesman for the agency said on Wednesday.
A total of 20 staff were abducted, first from a minibus on Tuesday, and then from a car on Wednesday, Mahdi al-Mashhadani of the Sunni Endowment said.
The employees had been stopped by gunmen in civilian clothes at a roadblock on the northern outskirts of Baghdad.
The Sunni Endowment has "suspended its activities in protest" at the kidnappings.
20 people killed
At least 20 people have died in a series of bombings and shootings on Wednesday, mostly in Baghdad, police said. They included an interior ministry official.
Six people were killed when a bomb hidden in a plastic bag exploded inside a vegetable shop in eastern Baghdad, police said. Five others died in three small blasts in al-Karrada district of central Baghdad.
Gunmen also stormed two markets, one in a Shia district of Baghdad, another in a village called Rasheed south of the capital, killing seven people.
Sixteen other bodies were found in separate parts of the country - apparent victims of sectarian violence.
The violence comes a day after a suicide bomber killed 53 people near a Shia shrine in the city of al-Kufa.
The United Nations has said the rise in sectarian bloodshed could destroy the unity government just two months after it took office.
"We hope there will be no civil war in Iraq," Ashraf Qazi, the UN envoy to Baghdad said. "Although the reality right now is that there is a very high degree of violence."
"The emerging phenomenon of Iraqis killing Iraqis on a daily basis is nothing less than a catastrophe," he said.
The UN has endorsed Iraqi data which suggests about 100 civilians are being killed daily across the country.