Several Klinik Nur Sejahtera have been using sterilising machines whose certificates of fitness expired between three months and nine years ago.
The Auditor-General's 2014 report said failure to renew the certificates could result in legal action being taken against the National Population and Family Development Board (LPPKN), which operated the clinics.
The report stated that improperly sterilised equipment could endanger users and noted how one clinic in Nusajaya, Johor, had a machine with a certificate that had expired on June 7, 2006.
The report revealed how contraceptives and pills were stored together with stationery, disposable items and unused assets at the board's storage facility when "a separate space should have been made available".
It also pointed out that the supply of medicine was not managed by registered medical officers or pharmacists while medical stock was being overseen by personnel with no relevant expertise.
"We discovered that due to a lack of planning, there was a procurement of RM5.41million (S$2 million) in medicines for the first two years - RM1.13mil over the permitted sum," it said.
The report raised concerns that no mechanism was put in place to confirm if applicants were in fact eligible for a special subsidised mammogram programme offered by the clinic.
The programme, together with another offering human papillomavirus (HPV) vaccination, is some of the main services provided by the clinic, which has 39 branches nationwide and six mobile bus facilities.
In response, LPPKN said they had issued a circular to all state directors to ensure that medicines were stored properly and standard operating procedure was adhered to. On the managing of medical stock, the board said it had ordered that only nurses were in charge of receiving the supply of contraceptives and medicines.