The investigation was ordered by Fife Council following widespread unrest in the community.
Residents had complained about the noise from high explosive blasting as well as vibrations and dust levels from the quarry.
In the report, which has just been published, it says complaints by the local residents about noise levels have been justified.
It added that operations at the facility based in the village of Leslie are "potentially a nuisance".
Council Leader Alex Rowley welcomed the report, saying: "It is a thorough independent analysis of the operation and the impact the Quarry is having on the local community.
"It confirms there has been an impact on a number of residents and everything possible must be done to address this now.
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"In particular, there is no doubt noise and vibration levels have caused distress, and whilst the report confirms the quarry is operating in line with planning consent and approved plans for managing noise, dust and vibration, there are specific recommendations that the current monitoring procedures should be reviewed. I agree.
"It's important we work on the next steps as soon as possible.
"The report will be going to the Executive next month and councillors will be asked to agree all the report recommendations and develop a response action plan in partnership with Skene and the community Liaison Group, ensuring the recommendations are being taken forward within 3 months."
Mr Rowley added: "I called for this independent report to ensure the difficulties facing local people were fully acknowledged, and to get further advice on what steps could be taken to improve things.
"I will, between now and the report going to the Executive, meet with local groups, the MP and MSP to hear first-hand their thoughts on the report.
"This report offers a new starting point and the only way forward is for the council and Skene to work in partnership with the local community. No improvements will be made without that."
The operators of the quarry, Skene Group, have said the report is "deeply flawed".
(JP/CD)
