The shelter, built along the lines of a similar one quietly trialled in the northern city of Shijiazhuang, will have an incubator, blankets, oxygen on standby and a button for parents to press to alert staff to the new arrival.
Authorities gingerly announced the plan after an embarrassing flurry of publicity this summer when three babies were abandoned over a few days around June 1, China's "Children's Day".
One was left in a rubbish bin and had suffered severe organ damage before being found, another was abandoned in a public lavatory and a third was left outside a hospital.
But the announcement of the baby shelter, literally the "baby abandonment island" in Chinese, provoked a national media outcry in which critics said it would encourage more parents to dump unwanted children.
Tang Rongsheng, the recently departed head of the city's social welfare centre, where abandoned children are taken in, said: "When we suggested the baby shelter in June, there was a lot of criticism that I was teaching people how to commit a crime.
"There have been a lot of wild accusations. Some have suggested that the number of abandonments will shoot up, others that baby traffickers will lie in wait outside the shelter and steal infants."
Six months after the initial announcement, the baby shelter outside Tang's social welfare centre remains unfurnished; the public outcry was strong enough to stall its completion. But Tang now has the support of Beijing. Baby shelters will be built nationwide, the vice-minister of the civil affairs bureau, Dou Yupei, has said.
Peng Xizhe, a professor at Fudan university who specialises in public policy and social development, said: "Abandoning a baby is a crime. But during the process of committing this crime, babies are the victims. Since the root of the crime ... cannot be solved in the blink of an eye, it is a good option to shift our focus to protecting those victims."
Tang said that there had been pressure in other Chinese cities, with the number of abandonments in inland provinces now higher than in Shenzhen.
"In Nanjing two infants died, one froze to death after being abandoned in a park and one starved," he said. "The higher-ups have asked us to accelerate our plan."
Inside the social welfare centre, which functions as the city's orphanage, 560 children, many of whom refer to Tang as "Father Tang", live in dormitories.
Half of the children would eventually be adopted, Tang said.
The other half were mentally or physically ill, and would be raised at the centre.
In the past decade, more than 3500 children have been abandoned in Shenzhen. But there is some good news - the number is decreasing as China grows wealthier.
"Usually it is single mothers, migrant workers, who do not know what to do, and who have no husband, money or support, who leave their children," Tang said. "Pregnancy screening also means fewer handicapped children are born."
He said the trend confounded the view that the shelter would encourage more abandonments.
"I don't think the numbers are going to rise," he said. "Parents only abandon their children if they are faced with an insurmountable problem."