The head and deputy and a lower official of the Chaoyang District education committee were "not doing their jobs", the municipal government said on its official social media account late Wednesday.
On Tuesday, Beijing police said a 22-year-old teacher at the kindergarten was detained for using sewing needles to punish children for not sleeping at the daycare, which is run by a company listed on the New York stock market.
But police said it found no evidence of other child abuse, including sexual molestation, after reviewing 113 hours of restored surveillance footage from RYB Education New World kindergarten.
Authorities said classroom video recordings were "damaged" because a staff member often turned off the building's electricity after school.
The investigation into the kindergarten was opened last week after parents said toddlers were given mysterious pills and had apparent needle marks.
But police also cast doubt on allegations that children were given unidentified pills.
Addressing a television report showing a clip of a student saying he was fed pills by teachers at the school, police said the child's father had admitted to "instructing" the child to say so.
The case prompted the State Council, China's top administrative body, to call for an "immediate" investigation into all kindergartens across the country.
The company directly operates 80 kindergartens and has franchised another 175 in 130 cities across China for children ranging from newborns to six-year-olds, according to its Nasdaq listing.
RYB Education has apologised for the incident, which was not the first to hit the company.
RYB apologised in April and suspended the head of a Beijing kindergarten after the Beijing News obtained videos showing teachers throwing a child on a bed and kicking another in the back.
In 2016, two teachers from a RYB kindergarten in northeast Jilin province were sentenced to 34 months in prison for jabbing children in the head, inside their mouths, and on their legs and buttocks with sewing needles, according to the People's Court Daily.
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