The fire on Learoyd Road in Hemswell Cliff, near Gainsborough, broke out at about 13:00 GMT on Thursday.
Residents were advised to keep their doors and windows closed to avoid “smoke drift”.
Three fire crews remain on site to dampen down and make sure it does not spread, Lincolnshire Fire and Rescue Service said.
The fire service’s group manager Ash Hildred said the blaze was caused when flames from a burning pile of woodchips spread to the bales in windy conditions.
“Where we are at the minute is making sure water is in place to prevent any further escalation if the wind changes,” he said.
Mr Hildred said crews would remain on site over the next few days to monitor the situation.
The site is a former RAF bomber base which closed in 1967 and was converted into industrial and agricultural use.
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