Tapanui farmer George Redditt raised the issue at the Clutha District Council's recent meeting.
He told councillors nodding thistle was an ongoing problem at a quarry operated by SouthRoads.
He understood nodding thistle at the quarry had been brought to the council's attention before, and the area had been sprayed.
''This should be monitored each spring and summer to prevent these invasive weeds from growing, and especially seeding. We are trying to keep these weeds out of our farms.''
Future council policy should see all quarries and gravel sites inspected and closed until operators were prepared and willing to operate in a ''best practice manner'', Mr Redditt said.
It appeared spraying was not the ''be all and end all'', councillor Ken Payne said.
Councillor John Cochrane said nodding thistle was ''not just a thistle'' but a ''noxious weed''.
''It has the potential to spread across the district,'' he said.
When the Otago Daily Times visited the quarry, scotch and nodding thistles were growing along the fenceline and seeds were starting to spread.
However, SouthRoads Otago regional manager Dean Elder said the thistles were sprayed earlier this year, and the company had been in touch with the Otago Regional Council to ensure they were following the rules.
''We are on top of it in terms of spraying and grubbing.''
SouthRoads did not have issues with nodding thistle at any other of its quarries, Mr Elder said.
Speaking to the Otago Daily Times on Friday, Mr Redditt said nodding thistle remained a big concern for farmers.
''I don't think people who are not farmers realise the gravity of the situation.''
Councillor Jeff McKenzie said landowners had to be vigilant and deal with nodding thistle early in the season to prevent seed spreading.
Nodding thistle is included in the Otago Regional Council's pest management strategy, and requires land occupiers to take responsibility for the control of pest plants and animals on their properties.
Under strategy, occupiers outside urban areas must destroy nodding thistle within 100m of a property boundary where the neighbouring property is clear of nodding thistle.
Nodding thistle
• Nodding thistle is an annual or biennial plant with flowering stems up to 1.5 metres tall.
• It has large crimson flowers which droop when mature.
• While similar to scotch thistle, nodding thistle is more erect and spiny and is considered the most aggressive of all thistles in its ability to invade pasture.
• It grows in dense patches preventing access to pasture.
• Each plant can produce up to 10,000 seeds.
• Resistant to drought, nodding thistle seed can remain viable for up to 20 years.
- Source: Otago Regional Council