Malaysia now accepts that Malaysia Airlines Flight 17 was shot down in Ukraine and its passengers were killed by a missile, its transport minister said Saturday.

The government is also "deeply concerned" that the crash site of the Boeing 777, which was flying from Amsterdam to Kuala Lumpur route with 298 people on board, hasn't been properly secured, Malaysian Transport Minister Liow Tiong Lai said told a news conference. (Follow the latest updates on the Malaysia Airlines crash in Ukraine.)

"The flight and its operators followed the rules. But on the ground, the rules of war were broken," Mr. Liow said, calling it an "unacceptable act of aggression."

Malaysian officials previously refrained from attributing the crash to a missile attack and called for more evidence even as U.S. intelligence agencies and Ukrainian officials said the plane was struck by a ground-to-air missile in the battle-torn region of Donetsk.

"This outrage cannot go unpunished," Mr. Liow said, calling for "those responsible to be found, and to face the full force of justice without delay."

The comments also come as international observers struggle to gain full access to the plane's crash site in the region controlled by pro-Russian separatists.

The site's integrity "has been compromised, and there are indications that vital evidence has not been preserved in place," Mr. Liow said, noting that any interference risks undermining the investigation into the crash.

Urging all involved to protect the site, Mr. Liow stressed that failure to stop such interference would be "a betrayal of the lives that were lost" and Malaysia won't tolerate "any actions that prevent us from learning the truth."

Write to Jason Ng at jason.ng@wsj.com