It said following an inspection in January, the ministry found the centre was breaching various regulations and licensing criteria.
Pitter Patter was allowed to stay open but the ministry had stripped it back to a provisional licence, with more conditions.
The letter did not tell parents what the conditions were, but encouraged them to read them at the centre.
In some of the complaints about the manager at the centre, former teachers were worried about how rough she was with children.
One teacher said she would push or pinch them as she walked past and would grab their wrists and yank them so hard staff were worried they would be dislocated.
Because some of the complaints related to food and safety, the ministry had requested the help of health officials.
"As several of the allegations that have been made in the complaints relate to the health and safety of children and the condition of the food being provided, a health report by a Public Health Protection Officer has been requested to support our investigations and to determine whether the service is meeting criteria relating to the premises and facilities as they relate to the health and safety standards."
It had also asked for a report from the Manawatū District Council to determine whether Pitter Patter's process in providing food for children meets the National Programme Level 2 of the Food Act 2014 and Food Regulations 2015.
The ministry said it would be offering staff at Pitter Patter professional development to "strengthen their practices and the delivery of education and care".
The ministry said it would continue to work with the Teaching Council, which was conducting its own investigation which was likely to take some time.
Complaints process
Teachers have criticised the ministry for its complaints processes.
One teacher who wanted to raise the alarm about what she saw at Pitter Patter said teachers would try to complain to the Ministry of Education, but confronted a system that demanded the initial complaint must be dealt with through the internal procedure first.
In this case, the process was to complain to the owner and manager at the centre - the very woman they wanted to raise concerns about.
"Many teachers wanted to say something but as the complaints procedure was to, in the first instance, go to the centre manager, they couldn't go to Pauline as she just swept complaints under the rug and then you were bullied and your job threatened for doing so.
"If you phone MOE with a complaint, they say to you, that you must follow the centre's complaints procedure.
"At Pitter Patter Education Centre, the complaints procedure was to in the first instance go to the centre manager.
"If you did, then you were reprimanded and nothing happened to your complaint. MOE were not interested in your complaint if you had not followed this."
Others said they were threatened with losing their jobs or the Teaching Council for speaking out.
However, the ministry said it often could and would investigate regardless of whether the complainant had followed internal processes.
Teachers from other centres also have raised concerns about the lack of transparency and the minimal investigation done when the ministry does act.
