Beit Almal, a West Bank business venture which owns a Nablus mall that Israel issued a closure order this month, lost 14 of its board members who were arrested in the overnight operation.
Meanwhile, the management denied any charge of raising funds for Hamas and refused to shut the five-storey complex.
The arrests had stoked tensions between Israel and Mahmoud Abbas, the Palestinian president, who is trying to claim his own authority in the West Bank since breaking with Hamas last year.
An Israeli military spokeswoman said the arrests were "part of a routine counter-terrorist operations," but had no further details.
Abbas said that Israeli operations seriously undermine his efforts to get Palestinians to support peace talks he is holding with Israel.
Hamas, which rejects peace talks with Israel, routed forces from Fatah, Abbas's political movement, to take over the Gaza Strip in June 2007.
Israel continues to step up campaigns against suspected Hamas assets in the occupied West Bank, where Abbas holds sway.