The Healthcare Environment Inspectorate (HEI) said improvements to standards of cleaning were needed after an unannounced visit to the Royal Hospital for Sick Children at Yorkhill in Glasgow.
The intensive care unit was highlighted as needing particular attention to improve standards of cleanliness.
Politicians yesterday said the failings were a concern for children and their parents. The health board said it had acted on the findings.
It follows a critical report earlier this month of the Royal Aberdeen Children's Hospital, where inspectors found evidence of stained mattresses and staff not washing their hands properly.
The HEI visited Yorkhill on 12 October, focusing on six parts of the hospital.
The inspectors raised concerns about waste disposal policies not being fully implemented, as well as worries about the disposal of "sharps" - equipment such as syringes.
On one ward clinical and domestic waste bins were full or overflowing, while a sharps bin with bloodstains was found in a clinical preparation room.
Some hospital staff were also found not to be complying with the dress code, by wearing jewellery, ties, watches and long sleeves.
Concerns were raised about cleanliness in most of the wards.
The report said: "In five out of the six areas inspected the standard of cleaning needs to be improved, particularly in the Fraser of Allander unit (a neurosciences ward] and the intensive care unit."
Inspectors found dust on window sills, above incubators and on the extension arms of equipment consoles near beds. They also complained of dirty soap dispensers in intensive care and dirty air vents in the diagnostic imaging unit.
HEI said the board must ensure equipment was cleaned in accordance with national guidance.It was also told to make sure staff were aware of the proper policy for cleaning toys on wards.
Susan Brimelow, HEI chief inspector, said: ""The inspection team observed good practice in engaging members of the public in cleanliness monitoring and the production of antimicrobial prescribing guidelines.
"However, the team did find that further improvement is required in the quality and monitoring of cleaning, raising awareness of the toy-cleaning policy and in implementing standard infection precautions in relation to waste management and sharp implements."
Jackie Baillie, Scottish Labour's health spokeswoman, said: "These failings are a concern and parents whose children are being treated at Yorkhill deserve better."
Rory Farrelly, NHSGGC's acute director of nursing, said: ""We have urgently put in place a comprehensive action plan that will ensure the requirements and recommendations highlighted in the report are addressed."
Health secretary Nicola Sturgeon said: "It's essential that our hospitals are cleaned and maintained to the highest possible standards, and that staff observe infection control procedures."