A space industry start-up that facilitated NASA's first rocket launch from Australian soil in more than a quarter of a century is being sued for nearly $5 million, with claims of bullying and discrimination filed against the company's director.

Equatorial Launch Australia (ELA) shot to national prominence earlier this year after the US space giant shot suborbital rockets from a spaceport it runs in remote north-east Arnhem Land.

Documents filed in the federal court, seen by the ABC, show that the company is now being sued by its former chief executive, Carley Scott, who is alleging she was unfairly dismissed from the firm in March.

In the documents, Ms Scott has also made a series of bullying allegations against ELA's current director, Michael Jones, who she also accused of making "belittling and discriminatory comments about women and Northern Territorians".

Mr Jones has also been accused of making "racist comments about Indigenous Australians".

He's alleged to have said to Ms Scott over time:

"There's too much spending on Aboriginal people, they get enough and are still crying poor."

"There should be no Aboriginal flag. Aboriginals never had flags. There should be just one Australian flag."

And: "The [Aboriginal land] permit system did not apply to him, as he is Australian and can go wherever he wants and doesn't need permission to go onto someone else's land."

He also accused of belittling Ms Scott as a woman, allegedly saying:

"You're part of the school of women club."

And asking: "Why do you think so many women get murdered before and after [Family Court cases]? It's the frustration the guys have that they're getting screwed."

ELA's space base lies on Aboriginal land near Nhulunbuy and has been sub-leased to the company by the powerful Gumatj clan.

In a statement, ELA said "personal accusations against Michael Jones were made as part of an earlier bullying claim in the Fair Work Commission, initiated by Ms Scott".

"It was responded to in detail as part of the Commission's usual process, but then further consideration of it was deferred several times by Ms Scott and it was ultimately withdrawn by her," the company said.

"Mr Jones vehemently denies the alleged statements attributed to him by Ms Scott and finds them reprehensible in nature."

NT government sticks by ELA

ELA's Arnhem Land spaceport was used by NASA to fire three rockets between June and July this year, but there have been no plans for future launches yet.

The NT government has been a backer of the Arnhem Land space base since its inception.