The board of Master Builders Northern Territory has stood down M+ J Builders director Michael John Buckley from its board after he and two others were charged with fraud offences against the Commonwealth in relation to procurement contracts.

The trio were arrested on Friday after an eight-month Federal investigation alleged they were rorting Department of Defence contracts valued at up to $71 million.

Mr Buckley, 41, the co-director of M + J Builders, Dallas Adrian Wynne, 48, a director of the Estate Works Program at the Department of Defence in Darwin, and his wife Natalie Jade Wynne, 40, the director of Transportable Solutions NT, appeared before Judge Jonathan Bortoli in Darwin Local Court on Monday, with all three granted bail to appear on February 17, with conditions including they surrender their passports.

M + J Builders is a majority Indigenous-owned company through a co-owner who has not been charged with any offences.

The Australian Federal Police raided businesses and homes across Darwin on Friday, allegedly seizing electronic devices including mobile phones and laptops, as well as documents, a gun, jewellery, $30,000 in cash and a small quantity of a substance believed to be cocaine.

The peak NT building body also stood down Mr Buckley, a board member, following his alleged involvement in the $71m Federal fraud.

In court on Monday prosecutors did not oppose bail, after the three were charged with dishonestly gaining a benefit from a Commonwealth entity, which carries a maximum 10-year jail term.

Mr Wynne was also charged with one count of abuse of public office, which carries a maximum jail term of five years.

The AFP alleged the three were part of a conspiracy to influence the awarding of Commonwealth and government tenders to M + J Builders and a subsidiary owned by the co-accused, with the intention of dishonestly gaining a benefit from the Commonwealth, namely the Department of Defence.

The agency on Saturday said Operation Panton Hill, run by the AFP and National Anti-Corruption Commission with no involvement with NT authorities, was launched in March after "a report of crime from the Department of Defence about irregularities identified through an internal investigation" into the roughly $71 million in contracts,

The joint operation - by the AFP and National Anti-Corruption Commission - did not involve the NT Police or NT authorities and investigations remain ongoing.