Mr Shepherd said the southerly change, forecast to bring showers on Tuesday evening and overnight, should help clear up the smoke.
The worst affected region was Sydney's north-west, with the highest air quality index level reaching 476 between 8am and 9am - more than double the hazardous level of 200.
Sydney's south-west was also badly affected by smoke, with an air quality index of 322. In Sydney's east, the air quality was almost at hazardous levels at 186.
In comparison, the air quality index for Beijing as of 7am was 81.
By 11am, the air quality index had reached 493 in Sydney's north-west, while it had dropped to "very poor" levels in the rest of the city.
Even though Beijing's air quality index reached 232 later in the morning, air quality in parts of Sydney was still twice as bad as China's capital.
Mr Shepherd said the RFS was working closely with the NSW Office of Environment and Heritage and the Bureau of Meteorology to keep the effect of hazard reduction burning on air quality to a minimum.
"We're trying to actually mitigate that as much as possible by changing burning patterns, changing lighting up times," he said.
"We are doing everything we possibly can to try and mitigate [the smoke], but we also need to be aware that we need to get this work done as well."
Smoke prompts health warning
In the 12 hours to midday, NSW Ambulance responded to 41 patients with asthma or breathing difficulties - almost double the 24 calls they received in the same time last Tuesday.
NSW Health is warning people with respiratory conditions including asthma to limit their time outdoors due to the poor air quality.
Director of Environmental Health, Dr Ben Scalley, said people should also avoid vigorous exercise and if possible stay in air-conditioned buildings.
“Healthy adults may also feel the effects of fine particles that can irritate the lungs, so it’s wise to reschedule or cut back on prolonged or strenuous outdoor activities when smoke levels are high," he said.
Dr Scalley said fine smoke particles can go deep into lungs, and can create a number of health problems.
“Smoke may aggravate existing heart and lung conditions and cause irritated eyes, as well as aggravate existing lung conditions, such as chronic bronchitis, emphysema and asthma," he said.
He said people with existing asthma or a lung condition who develop symptoms like shortness of breath, coughing, or wheezing "need to be vigilant with their treatment programs".
“Symptoms can occur for several days after smoke is inhaled," Dr Scalley said.
“If symptoms do not settle, seek medical advice. If you are on home oxygen treatment, continue as prescribed and if breathlessness worsens, contact your doctor."
Hazard reduction burns important ahead of fire season: RFS
While it has created plenty of smoke, Mr Shepherd said it was important for the RFS to get the hazard reduction burning done while they could.
"We live in the most bushfire prone land in the world, there is always an element of risk, and we try and mitigate that risk by doing hazard reduction burning."
He said with bushfires starting earlier and earlier, it was important for landholders to make sure their land was also prepared.
"In possibly eight weeks we could possibly see fires again," Mr Shepherd said.
"Yes, we're doing as much as we possibly can, but as well there’s an onus on property owners to ensure that their properties are prepared and they have a plan."
Rachel Clun is a reporter at the Sydney Morning Herald. She was previously a reporter with the Brisbane Times and Domain.
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