The raid occurred 35km south of the northern city of Kunduz on Thursday, until now deemed a secure area.
President Hu Jintai demanded the Afghan government and the UN mission carry out a thorough investigation.
Some of the 100 or so Chinese workers at the site, many of them from the eastern Chinese province of Shandong, had only arrived at the compound site on Tuesday.
Foreign Ministry spokesman Liu Jianchao told a regular briefing the government was also pushing for Kabul to "punish the attackers and ensure the safety of Chinese workers and other staff in Afghanistan".
Kunduz governor Muhammad Umar blamed the raid on rebels bent on destabilising the government of interim president Hamid Karzai.
Umar said the attackers used assault rifles, rocket-propelled grenades and hand grenades in the attack at around 20:30 GMT on Wednesday. One Afghan guard was also killed and four Chinese were wounded.
A Taliban spokesman, Hamid Agha, denied that the attack had anything to do with the Islamist group. "We were not behind this, we have not done this."
Liu said Chinese projects in Afghanistan - including the renovation of a hospital in the capital Kabul - would go ahead regardless of the attack.
"The Chinese government and people will not yield to any terrorism," he said. "It should be a lesson for us. We should take more effective measures to ensure the safety of Chinese nationals abroad."