Police cordoned off the building and the adjacent area, and the GKNB state security service said they were investigating the bombing that occurred around 1000 local time (0400 GMT).
China condemned the assault and urged the Kyrgyz authorities to "quickly investigate and determine the real situation behind the incident.
"China is deeply shocked by this and strongly condemns this violent and extreme act," foreign ministry spokeswoman Hua Chunying told a regular news briefing in Beijing.
Three embassy staff suffered minor injuries and had been taken to hospital, but no organisation had yet claimed responsibility, Hua said.
China's state news agency Xinhua said five people were wounded: two security guards and three Kyrgyz nationals working at the embassy.
Authorities in Kyrgyzstan, a mostly Muslim former Soviet republic of 6 million people, routinely detain suspected Islamist militants they accuse of being linked to Islamic State, which actively recruits from Central Asia.
An anti-Chinese militant group made up of ethnic Uighurs - a Turkic-language speaking, mainly Muslim people, most of whom live in China's Xinjiang region - is also believed by some to be active in Central Asia, although security experts have questioned that.
In 2014, Kyrgyz border guards killed 11 people believed to be members of that group who had illegally crossed the Chinese-Kyrgyz border.
Attacks on Chinese missions abroad are rare, although its embassy in Belgrade was hit in error during the NATO bombing of Yugoslavia in 1999.
An Islamist militant attack on a hotel in Mali in 2015 killed three Chinese citizens, and this year a Chinese U.N. peacekeeper was killed in an attack, also in Mali.
In Pakistan, Chinese workers have occasionally been targeted by what police say are nationalists opposed to its plans to invest tens of billions of dollars in a new trade route to the Arabian Sea, part of its "One Belt, One Road" project to open new markets via Central Asia, South Asia and the Middle East.
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