Representatives of the Healthcare Environment Inspectorate (HEI) found blood on bed rails and bed controls, contaminated incubators and rusty scrubbing-up sinks after visits to Aberdeen Maternity Hospital in September and October.
The chief inspector issued seven requirements that must be met.
Theresa Fyffe, director of the Royal College of Nursing (RCN) Scotland, said the report raised serious concerns that had to be addressed if the health board was to reassure parents-to-be the hospital could look after mothers and babies "to the high standard they expect and deserve".
NHS Grampian said the issues had been tackled urgently and plans for a replacement facility hospital needed to be drawn up in the next few years. It said the report highlighted shortfalls in the operating theatre and that a replacement is to open "soon".
One inspection, which followed two earlier visits in which significant concerns had been raised about the cleanliness in the neonatal unit, found body fluids on the cot sheet in the theatre, significant dust in an area of the theatre's anaesthetic room and an oxygen mask that was broken and could not be effectively cleaned.
Inspectors first visited the maternity hospital on August 21. Due to significant concerns raised about the cleanliness in the neonatal unit they carried out a follow-up inspection on September 5, followed by another unannounced visit to the theatre and procedure room on September 17.
The report reveals that, during their initial visit, inspectors found three of the seven mattresses they checked in the labour ward and two other maternity wards were contaminated with blood or other body fluids.
HEI inspectors also identified a number of problems with the storage of expressed breast milk.
Susan Brimelow, the HEI's chief inspector, said: "I am very disappointed at the findings and, because of the serious nature, I escalated my concerns to Scottish Government. Every patient coming into hospital should expect their local hospital to be clean and safe."
The HEI's seven-point plan for urgent improvements included a demand that expressed breast milk is stored appropriately and documentation reflects best practice, ensuring the storage of expressed breast milk is managed in a way that reduces the risk to patients.
NHS Grampian has also been ordered to ensure senior charge nurses and senior charge midwives have accountability for ward cleanliness and to review the storage areas in the neonatal unit to allow for stock rotation of the equipment required for the department.
Health Secretary Alex Neil said: "I am extremely disappointed families in NHS Grampian have been let down in this way.
"That is one of the key reasons why we set up the Healthcare Environment Inspectorate - to ensure that we continue to drive up standards of care and protect patient safety at all times.
"I have received assurance from NHS Grampian that it takes the recommendations very seriously and I welcome its action plan. We will be working closely with NHS Grampian to monitor progress."