The air quality index, which measures the concentration of poisonous particulate matter, has hit 331 in parts of Delhi on a scale where anything above 100 is considered unhealthy by the Central Pollution Control Board.
Officials said the burning of some crop stubble in the northern states of Punjab and Haryana caused pollution levels to rise, even though the practice was banned and federal authorities have threatened to punish anyone doing so.
"This is also the time when pollution levels are likely to be extremely high, with poor air quality," it said in a statement, warning that this could aggravate asthma or another lung disease, such as chronic obstructive pulmonary disease.
Some participants wore masks in last year's race. A high level of PM 2.5, or tiny particulate matter that can reach deep into the lungs, can increase blood pressure and even cause a stroke, the foundation added.
Another pollutant, PM10, was a direct threat to runners, as it is inhaled in large amounts when people breathe through the mouth while running, although it is filtered out through the nose when breathing normally.
Vehicle exhaust emissions in a city with limited public transport, emissions from thermal power stations and swirling construction dust are New Delhi's main pollutants.
In winter months crop burning in the farm states surrounding the landlocked capital city worsens the situation.
The chief minister of Punjab, Amarinder Singh, told media he had seen plumes of smoke from fields during a helicopter flight last week. But he said the state was doing all it could to stop the practice.
(With inputs from agencies.)