A lone protester shouted slogans and threw a glass bottle and a traffic barrier towards the embassy gate, before he too was escorted away.
In Shanghai, around 20 people waved Chinese flags, hoisted banners that read "return my Diaoyu Islands, release my brave warriors," and shouted slogans outside the Japanese consulate before being escorted away by police.
An editorial in the People's Daily, the Chinese Communist Party's mouthpiece, upbraided Japan and called on Tokyo to reflect on its actions "from a deep level".
"A country... that persists in... political wrongdoings and that cannot stand face-to-face with the international community cannot become a respected country no matter how much its economy grows," it said.
The case is a delicate one for Japan, which has to balance popular irritation at the landing with vehement demands from China for the immediate release of the group.
The decision to deport the 14 was widely expected, with Tokyo looking to avoid a repeat of the diplomatic calamity of 2010 when it held a Chinese trawlerman for two weeks after he rammed coastguard vessels.
Japan was widely criticised as having caved in to Chinese pressure and being forced into releasing the man after Beijing halted high level contacts and stymied trade.
The group of activists had sailed from Hong Kong on Sunday to the archipelago, where pictures show they raised Chinese and Taiwanese flags. Taiwan also claims the islands.
In 2004, when a group of Chinese activists landed on a disputed island, then prime minister Junichiro Koizumi ordered their deportation after two days.
The renewed dispute over the islands comes as Japan's relations with South Korea have become increasingly frayed after President Lee Myung-Bak last week visited islets controlled by Seoul but claimed by Tokyo.
Nearly 200 people held a rally in front of the South Korean embassy in central Tokyo, protesting against the visit and calling on Lee to apologise to the Japanese emperor.