Xi warned Mattis on Wednesday that China "cannot lose even one inch of the territory left behind by our ancestors."
The president had already approved 33 different projects to upgrade and modernize military capacities.
The missiles reappeared in "exactly" the same position as where they were prior to disappearing.
China says it "won't be scared" after the U.S. flew two B-52 bombers over the Spratly Islands on Tuesday.
Lieutenant General Kenneth McKenzie said the U.S. would continue to conduct operations around the Chinese bases despite criticism from Beijing.
A Chinese Foreign Ministry official likened U.S. complaints about China's militarization of the South China Sea to "a thief crying 'stop thief.'"
Chinese-American relations in Asia have been strained by Beijing's increasingly determined military policy, especially in the South China Sea.
Duterte has recently faced criticism for his silence about China's increasingly aggressive posture in the disputed waters.
The Chinese Defense Ministry said "it is impossible to shake China's determination to safeguard its sovereignty and security interests."
The "Big Three" of China's seven man-made islands Subi, Mischief and Fiery Cross all host a range of military infrastructures, satellite images show.
"China's continued militarization of disputed features in the South China Sea only serve to raise tensions and destabilize the region," the Pentagon said.
Only the U.S., Russia and some European Union countries have such advanced stealth capabilities.
China says it has "the resolve, confidence and ability" to defend its territorial integrity by reuniting Taiwan with the mainland by force.
China is investing in military bases to project its power across the Asia Pacific and there's little the U.S. can do to stop it.
Chinese President Xi Jinping appears to be losing patience with Taiwan's ideas of independence and he's turning up the heat with military exercises.
"The Americans are our friends…. They can help us to deter any threat," said Lieutenant General Rolando Bautista of the Philippine army.
As a trade war looms, China says it won't tolerate U.S. arms sales to self-ruled Taiwan.
China's militarization of its island bases signified Beijing's determination to assert its territorial claims, regardless of U.S. opposition.
In contrast to the allegedly scaled-down U.S. and South Korean drills, experts have commented on the unusually large formation of Chinese warships heading to the South China Sea.
Russia has agreed to a new military cooperation roadmap with Vietnam which will allow joint military training and maneuvers.
The carrier is a potent symbol of the ambition of China's modernized military.
China is holding drills bigger and more frequent than before at a time when it's making it clear that it will take Taiwan back by force if necessary.
Marine Corps will send more than 1,500 troops to Australia to train with several nations that claim the same waters China wants to commandeer as its own.
Cybersecurity firm FireEye warns groups linked to South China Sea dispute being targeted.
China's foreign minister said that it was U.S. shows of force that were destabilizing the region, not Chinese island building.