Intel pledged Thursday to adopt a broad regime of air quality monitoring and public reporting of atmospheric pollutants, settling with environmental groups that had threatened to sue over the company’s failure to disclose fluoride emissions at its Washington County computer chip factories.

State regulators and the company said fluoride emissions were within safe levels, but the lapse threw Intel’s permitting status into confusion and cast a shadow on the largest construction project in state history.

Thursday’s deal requires Intel to assess health risks from atmospheric emissions at its massive Oregon factories, monitor air quality and report the results publicly. It comes on the heels of a $143,000 fine issued last month by state environmental regulators.

Intel still faces additional steps, beginning with a “good neighbor agreement” to be negotiated with groups representing residents near its factory. And it eventually needs a new air quality permit from the state.

Still, Thursday’s deal removes a legal cloud from the company and establishes a framework for monitoring its environmental impact going forward.

“This is really looking at community concern,” said John Krallman, an attorney for Neighbors for Clean Air, which joined the Northwest Environmental Defense Center in negotiating the pact with Intel.

“There were a lot of people saying ‘Oh my gosh, this is a high-tech industry and they’re using a lot of dangerous-sounding chemicals,’ and they are,” Krallman said. “What this agreement really is about is opening up the process and transparency.”

The company began work in 2010 on the first of two new research factories, known collectively as D1X, with a combined price tag somewhere north of $6 billion.

As Intel sought environmental permits for the project last year, it acknowledged that it had failed to report fluoride emissions at its Oregon factories, a disclosure that is required under the state’s environmental laws.

State regulators and the company said fluoride emissions were within safe levels, but the lapse threw Intel’s permitting status into confusion.

Neighbors for Clean Air responded by filing a notice of intent to sue the company to enforce federal environmental standards. The watchdog group claimed the company had failed to get the correct D1X permit — which would have required more vetting and a public hearing process — because it did not report airborne fluoride emissions to the state.

Thursday’s settlement resolves that legal issue and moves far beyond the narrow fluoride issue by creating a broad regime for Intel air quality monitoring and reporting under California standards more rigorous than those in Oregon.

The deal establishes an Air Quality Advisory Committee, with members appointed by Neighbors for Clean Air and the Northwest Environmental Defense Center, which will oversee implementation of the agreement.

The deal requires Intel to monitor and report air quality at its factories in Hillsboro and Aloha, and to fund third-party air quality monitoring elsewhere in the community. A risk assessment will identify particular hazards and a manner for addressing them, but it does not require Intel to eliminate them altogether – provided they are in compliance with environmental laws.

While Thursday’s deal expires at the end of 2015, the parties will begin work shortly on a good neighbor agreement that would incorporate the terms of the settlement. Neighbors plan to ask the DEQ to incorporate that agreement into Intel’s air quality permit, giving it the force of law.

Intel spokeswoman Chelsea Hossaini said the company knows it has lost some trust in the community over the fluoride issue, and said the agreement represents a sincere effort to repair that breach.

“We’re always striving for continuous improvement and will take the results of the environmental testing seriously,” she said.

Thursday’s deal represents “a good set of first steps” on the road to a good neighbor agreement, said Linda Peters, a former Washington County commissioner now with the Washington County Citizen Action Network. She said it establishes a framework for frequent monitoring of Intel’s emissions, disclosure of the results and some assurance that the company is working to keep hazards out of the air.

“I’m feeling we got as good an agreement as we could have gotten,” Peters said, “They are committing to put public health somewhat higher on their priority list.”

Hillsboro Mayor Jerry Willey applauded Intel, saying he’s “pleased that Intel’s working with the neighbors and with the DEQ.”

“I’m glad that Intel made DEQ aware of the air quality emissions issue and have worked hard to resolve it,” Willey said.

Update: This article has been updated with additional context and comment.