Yes.
The government considered this film to be Zionist propaganda and banned it.


Background
Schindler’s List is based on the true story of Oskar Schindler, a German businessman and Nazi party member, who rescued more than a thousand Jews from the concentration camps and execution during World War II.

Malaysia’s Film Censorship Board, a government entity, banned the film calling it “propaganda with the purpose of asking for sympathy, as well as to tarnish the other race.”

The Malaysian Prime Minister in charge of the censorship board, Mahathir bin Mohamad, was allegedly an
anti-Semite who feared that Zionists would take over Arab territories. He supported Palestinian self-rule in the Israeli-Palestinian conflict. The centuries old conflict involves disputed land rights in the West Bank territory and Gaza Strip between both countries. It is tied into deeply held religious beliefs about sacred rights to the land, historic foreign conquest and exile, and larger political issues in the region.

Although Malaysia has freedom of religion, Islam is the country’s official religion and clashes between religious groups are common.

Eventually the Malaysian government said the ban would be reconsidered if director Steven Spielberg deleted scenes the board found objectionable. Spielberg refused arguing that the film needed to be shown fully intact and depicted actual events that should not be watered down.

Other Islamic countries, such as Jordan, also refused to show the film.

One Official Wants Ban Reconsidered : Rebukes for Malaysia Over 'Schindler's List'
New York Times, March 24, 1994

Islamic Nations Move to Keep Out 'Schindler's List'
New York Times, April 7, 1994

List of all Films Banned in Malaysia
Internet Movie Database

Film Pushes Malaysian Censorship Boundaries, but Not Too Far
New York Times, October 28, 2010

Malaysia primed for Munich release
The Guardian. January 13, 2006

Central Intelligence Agency, World FactBook. Malaysia.
Central Intelligence Agency

Freedom in the World, Malaysia 2011
Freedom House