The Mossmorran chemical plant will be the focus of a joint investigation by the Health and Safety Executive (HSE) and Scottish Environment Protection Agency (Sepa).
The inquiry was announced on Friday after Sepa served final warnings on operators ExxonMobil Chemical and Shell UK.
Operating permit variations will also be served next week, requiring the companies to strengthen controls on noise and vibration.
It follows prolonged flaring in June last year, which Sepa described as “preventable and unacceptable”.
Residents from miles around complained of disruption from the site, comparing the rumbling to the noise of a jet engine.
Some said the flaring, which went on for nine days and is part of the plant’s safety system, kept them awake and raised concerns about the impact on residents’ health.
Further unplanned flaring events in October 2017 and March and May this year are under investigation by Sepa.
The agency’s chief executive Terry A’Hearn announced the joint inquiry following a meeting in Kirkcaldy with locals and politicians.
He said: “We were clear that unplanned flaring in June 2017 was preventable and unacceptable and we issued final warnings to both companies in that regard.
“Despite that, communities have endured further unplanned flaring in October, March and again in May.
“We’ve listened carefully to community calls for a root and branch review and today’s announcement of a joint investigation by the Scottish Environment Protection Agency and the Health and Safety Executive will examine issues at both sites.”
He added: “It’s right that people want to know more about October, March and May flaring incidents.
“That said, people want action not words which is why I’ve come personally to explain why these incidents remain under investigation and why we need to avoid prejudice to future enforcement action.
“We’re listening to the community and it’s important the companies do too.”
Mid Scotland and Fife Labour MSP Alex Rowley said: “People will be pleased to see the whole issue is being taken far more seriously.
“One of the key questions is why does the plant keep breaking down? It is a 30-year-old plant.
“We also need to keep pushing for air quality monitoring in all the communities around the plant and further afield, including Dunfermline and Kirkcaldy.”
Green MSP for Mid Scotland and Fife Mark Ruskell welcomed the probe but agreed there were questions to be answered about the safety and maintenance of the aeing plant.
He said: “Standards have moved on a great deal since the plant opened in 1985, and the regulation and enforcement needs to constantly develop too.
“Although the plant operators have improved their communication and been open about the technical causes of the recent flaring, there remain serious questions about why these incidents occurred in the first place.
“There are ongoing concerns about the maintenance and safety of this ageing plant, and if it’s shown that the repeated flaring is down to poor maintenance, there needs to be legal consequences”.
Labour MP Lesley Laird said the inquiry was “a victory for residents”.
She added: “It shows the power people have when we get all the right people in a room.
“I’d like to extend my thanks to community representatives in the group for having the faith and commitment to take part in the work we’ve been doing.
“There’s still considerably more to be achieved but now we have the attention and co-operation of all key agencies. We will continue in our endeavours working to secure the best positive outcomes for communities surrounding Mossmorran.”
A spokesman for ExxonMobilk said: “We are committed to being a valued member of the local community and were pleased to participate in today’s community meeting. We are engaging positively with community representatives, other local bodies and the regulators to address any concerns about our operations.
“We comply with all applicable laws and regulations, and fully recognise the importance of regulating the operation of a plant of the scale and complexity of FEP in order to minimise the impact on the surrounding communities and the wider environment.
“Our operations are governed by our permit from SEPA and we have a longstanding record of good compliance with our operating permit.
“We will be working with SEPA, the HSE and local interests to ensure our operating scope is clearly defined and understood.”
A Shell spokesman said: “Shell UK Limited was aware of SEPA’s intent to issue a permit variation and we have been working with the regulator to agree the areas to be addressed.
“We will co-operate fully in a joint investigation as required, and we will seek to better understand our role in it.”
“We were pleased to participate in the third Mossmorran Community meeting today. We welcomed the opportunity to provide an update on our activities, and discuss how we can help address community concerns with other interested parties.“