Kimberley Land Council has apologised and committed to repaying 630 current and former employees $1.36 million after an internal audit uncovered underpayments.

Kimberley Land Council disclosed the underpayment, which occurred between July 1, 2016 and October 22, 2019, on Monday after a payroll audit revealed the $1.36 million error which excludes lost interest and superannuation.

The land council lays claim to being the peak Indigenous body in the Kimberley region where it works with Aboriginal people to secure native title recognition, conduct conservation and land management activities, and develop cultural business enterprises.

It identified the underpayment for 630 staff under its 2014 enterprise agreement where payments fell below the mandated base rate compared to the modern award rate.

Kimberley Land Council said it had received external legal advice in 2018 stating its payments were compliant with wage obligations but subsequent legal advice contradicting the initial advice led to an in-depth audit which uncovered the error.

Current and former workers are being contacted by the land council which has apologised.

"Our priority is to pay the identified amounts to our current and former affected staff members in a timely manner and ensure this does not happen again," chief executive Tyronne Garstone said.

The Kimberley Land Council is one of the biggest employers in the northern Western Australia region with about 130 staff across its divisions.

It voluntarily disclosed the error to the Fair Work Ombudsman.

A spokeswoman for the ombudsman said it was conducting inquiries following the report of underpayments.

Employees who worked at the organisation between July 2016 and October, 2019 are encouraged to make contact.

William Ton - AAP