The comments, which come just three days after President Xi Jinping was in the US for talks, suggest a hardening stance in Beijing to America’s unexpected intervention in the country’s civil war.
China’s Foreign Ministry spokeswoman Hua Chunying was quoted by the Russian news agency Tass as saying Beijing opposed the missile strike.
Speaking on Monday, she said: “China has always called against using military force in international relations and for preserving territorial sovereignty.
"It is up to the Syrian people to decide on Syria’s future.”
Those remarks go further than comments made by Ms Chunying on Friday, when she said Beijing hoped “all sides will stay calm and exercise restraint to prevent the escalation of tension”.
The diplomatic crisis was triggered by a suspected nerve gas attack by Syrian President Bashar al-Assad on the town of Khan Sheikhoun, which left more than 80 people dead.
In response, Donald Trump gave the order for the launch of 59 tomahawk cruise missiles aimed at a Syrian air base said to house the chemical agents used in the attack.
The air strike was launched as Donald Trump hosted Mr Xi at his Mar-a-Lago resort in Florida.
He used the talks to press Mr Xi to do more to curb North Korea's nuclear programme, and the meeting was largely judged to be a success, particularly by Chinese state media, who said the event was proof confrontation between the two powers was not inevitable.
Mr Trump tweeted after the Florida summit that the meeting had been “tremendous... goodwill and friendship was formed”.
However, the cordial tone of the meeting was not replicated in the response issued by Russia and Iran to the cruise missile strike.
The alliance supporting the Syrian President warned the US they would “respond with force” if their own “red lines” were crossed in Syria.
“What America waged in an aggression on Syria is a crossing of red lines. From now on we will respond with force to any aggressor or any breach of red lines from whoever it is and America knows our ability to respond well,” the group’s joint command centre said.
China’s reaction to the missile strike is being closely watched, both for the impact it could have on its relationship with North Korea, and how it might affect rapidly shifting geopolitics in the region.
In February, Russia and China vetoed a UN Security Council resolution that would have authorised punitive actions against the Syrian government.
It came after a joint investigative team from the United Nations and the Organisation for the Prohibition of Chemical Weapons watchdog group concluded that the Syrian government carried out chlorine gas attacks three times in 2014 and 2015.
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