It was followed by a B-52 bomber flyover of the Spratlys this week, which the US said was part of a "routine training mission."
Two US defense officials told CNN that it is very unlikely China has totally removed the missile system. Instead, the US has assessed that the Chinese have likely concealed them inside buildings.
On Wednesday, Beijing said it was the US, not China, which was militarizing the region.
"I hope the US can explain to everyone: Isn't it militarization when you send attacking weapons like the B-52 bombers to the South China Sea? Were the B-52s there for freedom of navigation and overflight? If someone frequently flexes his muscles or snoops around near your house, shouldn't you raise your alertness and improve your defense capabilities?" Chinese Foreign Ministry spokeswoman Hua Chunying said at a regular press conference.
"China will not be intimidated by any planes or ships. We will only be firmer in our resolve to take all necessary measures to safeguard our sovereignty and security as well as maintain peace and stability in the South China Sea."
Missile systems
Those have now disappeared, in what ISI said could indicate a decision by Beijing to remove them, or redeploy them to other parts of the South China Sea.
"On the other hand, it may be a regular practice," the firm said. "If so, within the next few days we may observe a redeployment in the same area."
Other analysts agreed, saying it could be because the missiles were not suited to deployment where they might be vulnerable to salt water damage, and therefore may have required replacement or repair.
"Due to the corrosive effects of salt and humidity in the islands, HQ-9 missile systems must be removed and sent back to the mainland for maintenance periodically," said Timothy Heath, a senior defense analyst at the Rand Corporation.
Derek Grossman, another Rand defense analyst, said he was "highly skeptical that Beijing has completely and permanently removed (the missiles) from the region."
He said it might be the case that Beijing has "purposefully removed and stored the missiles out of sight for the time being to bolster its narrative of peaceful activity in the South China Sea. Then, when criticism dies down, it can easily redeploy these systems."
Rising tensions
In recent months US officials have said that the Chinese military has deployed anti-ship missiles, surface-to-air missile systems, and electronic jammers to contested features in the Spratly Islands region of the South China Sea.
China also recently landed a nuclear-capable H-6K bomber aircraft on Woody Island for the first time.
After the US raised objections about the deployment of missile launchers to the Spratlys, China said "necessary national defense facilities" had been added to the islands, reiterating Beijing's "indisputable sovereignty" over the territory.
"Make no mistake: America is in the Indo-Pacific to stay. This is our priority theater."
Ian Storey, a senior fellow at the Institute of Southeast Asian Studies, said it was unlikely China's removal of the missiles was related to criticism at the Singapore conference.
"The most plausible reason is that the missile deployment was always going to be on a short-term rather than a permanent basis," he said. "I'm sure they will be redeployed at a later date, either in the Paracels or in the Spratlys."
CNN's Begona Blanco Munoz, Sarah Faidell, Steven Jiang, Joshua Berlinger, Barbara Starr and Ryan Browne contributed reporting.