The banners carried the message “Welcome to the Philippines, Province of China,” in English and Mandarin.
The Metro Manila Development Authority, which maintains the footbridges, said it did not issue permits for the banners and personnel have been instructed to take them down.
The banners appeared as the country marked the July 12, 2016, ruling of an international arbitration court on a case filed by the Philippines which stated that China has no legal or historic basis to its claim to almost the entire South China Sea.
Former solicitor general Florin Hilbay, who led the Philippines’ legal panel in the arbitration case, tweeted the banners were “Not funny.”
“Whatever the motives may be, it's really not funny, especially on this particular day,” he added.
Aside from the Philippines and China, parts of the sea, which is a key shipping lane believed to be rich in mineral and marine resources, are also claimed by Vietnam, Malaysia, Taiwan and Brunei.