The decision by the center's board of directors came a day after former first lady and art patron Imelda Marcos joined politicians and Roman Catholic church leaders in denouncing the exhibit.
The board said it made the decision because of "an increasing number of threats to persons and property," including the artists and the cultural center staff.
It said the threats increased after critics vandalized an installation by removing a wooden penis from a poster depicting Jesus Christ.
The exhibit by contemporary Filipino artists including Mideo Cruz prompted heated debate about freedom of expression, with President Benigno Aquino II describing it as offensive to the 85 percent of Filipinos who are Christian like him.
Aquino said he reminded the cultural center that freedoms should be ennobling, and "when you stoke conflict, that is not an ennobling activity."
One sculpture portrayed Christ as Mickey Mouse, while a collage combined an image of Christ with pictures of celebrities, commercial products and characters from children's TV shows. Condoms, rosaries and wooden penises adorned the wall.
The exhibit, which opened in June, had been scheduled to run through Aug. 21.
The cultural center said Cruz's art had been exhibited without the same degree of controversy since 2002 in various other venues, including the Jesuit-run Ateneo de Manila University and the Vargas Museum at the state-run University of the Philippines.
An introduction to Cruz's work said it "speaks of idolatry and the deconstruction of neo-deities."
It described the cross and the image of Christ as representative of Filipinos' cultural past because the Southeast Asian nation was ruled by Spain and conservative Catholic friars for almost four centuries before it was administered as an American territory for 48 years.
Cruz declined to comment on the closure of the exhibit.
National artist Bienvenido Lumbera, who chairs a group called Concerned Artists of the Philippines, said the cultural center's decision would open it to pressure "anytime an art object raises the ire of certain sectors."
