The Healthcare Environment Inspectorate (HEI) said University Hospital Ayr was generally clean and well maintained but an unannounced visit on April 1 had identified "significant issues" in the emergency care unit.
The team found blood and body fluids on equipment which included trolleys used to transport patients, the drawers of a storage unit containing opened packages of swabs and a tourniquet - a mechanical device used for the temporary control of the circulation of blood.
Inspectors also uncovered "significant amounts of thick grey dust" on worktops, shelving, cupboards, lamps and on the edges of flooring.
The report said: "During our inspection of the A&E department, we found that the standard of environmental cleaning was poor.
"We found that several pieces of patient equipment in the A&E department were stained with dried blood.
"We informed a nurse of this contamination, who then cleaned the blood spillage using inappropriate cleaning products and procedures."
Inspectors alerted senior management and requested immediate action before returning on April 11, when they found "significant improvements" had been made to the standard of cleaning.
HEI, which carries out around 30 inspections a year in Scotland, issued six requirements and one recommendation in its report.
The hospital must ensure that all patient equipment in the A&E department is cleaned and ready to use in accordance with standard infection control precautions and review its systems to ensure that cleaning standards consistently meet the NHS Scotland specifications.
It was also called on to ensure all staff are implementing infection control precautions in the management of blood and body fluid spillages.
The report said: "NHS Ayrshire & Arran must address the requirements and the necessary improvements made, as a matter of priority."
The health board said A&E staff had responded swiftly to the inspection findings.
Chief executive John Burns said: "The report notes staff's good awareness, knowledge and understanding of their roles and responsibilities for infection prevention and control in the ward environment, and staff spoke positively about the level of communication with domestic services and felt able to influence domestic cleaning.
"However, there were some areas where the inspection team noted that improvements could be made.
"These areas mainly related to the standards of cleaning within the accident and emergency department and immediate steps were taken to address these during the inspection.
"I want to reassure the public that we take prevention and control of infection extremely seriously; and we have increased our focus on our own programme of unannounced inspections and audits to reinforce those provided by the Healthcare Environment Inspectorate.
"Our accident and emergency staff work in a hugely challenging environment around the clock and I am very grateful to them for their swift and positive response to the inspection.
"As part of the £27 million Building for Better Care programme, work has started on a new, fit-for-purpose emergency department at University Hospital Ayr.
"The new department will provide a much enhanced physical environment which will help staff to deliver a range of quality improvement programmes to improve the experience of patients who have to attend hospital in an emergency."
Health Secretary Alex Neil said: "Patients and the public deserve to have complete confidence in the cleanliness of Scottish hospitals and the quality of NHS services - that is why we have introduced these inspections as one of a range of measures to tackle healthcare associated infections.
"Whilst I am pleased to note that University Hospital Ayr is making good progress against the quality improvement standards, it is clear that there are still areas for improvement at University Hospital Ayr.
"NHS Ayrshire & Arran takes these recommendations very seriously and I welcome NHS Ayrshire & Arran's improvement action plan, which sets out how it intends to resolve the issues raised as quickly as possible.
"HEI will continue to inspect the hospital in the future to ensure lessons are taken forward to ensure the cleanliness of hospitals and the quality and safety of services for patients.
"Tackling and minimising healthcare associated infections is a key priority for the Scottish Government."