Andrew “Twiggy” Forrest’s Fortescue Metals Group should appear sooner rather than later before a parliamentary inquiry into the destruction of Juukan Gorge after two days of “quite damning” evidence from traditional owners regarding the company’s conduct in the Pilbara, the inquiry’s chairman has said.

“In light of recent evidence over the past few days it is very much in their interest to present their side of the story,” the chairman, Warren Entsch, told Guardian Australia.

Entsch said the federal joint standing committee on northern Australia had reached out on several occasions to Fortescue and was waiting for the company to respond.

“We will continue to reach out to them because it is absolutely critical they have the opportunity to respond,” the Liberal National party MP said.

The parliamentary inquiry was set up after Rio Tinto destroyed a 46,000-year-old Aboriginal sacred site in the Pilbara in May. The committee was tasked with examining how the destruction came about, the processes that failed to protect the site, and the legislative changes required to prevent such episodes from recurring.

Over the past two days, Aboriginal traditional owner groups have made serious allegations about their dealings with Fortescue.

Eastern Guruma Aboriginal traditional owners said the company was withholding $1.9m in royalties because they had asked “for information about their plans” for nine mining leases in areas with significant and sacred sites.

“We have asked FMG to reconsider their position and they have advised us that they will only pay the royalties when we sign off on the mining leases,” the Wintawari Guruma Aboriginal Corporation’s Joselyn Hicks told the inquiry on Tuesday.

In reply, Fortescue said it took its relationship with traditional custodians seriously.

“We are committed to open and transparent engagement to facilitate the outstanding royalty payment, in accordance with the contractual agreement and the obligations of both parties,” said its chief executive, Elizabeth Gaines.

On Monday the Puutu Kunti Kuurrama and Pinikura people, the traditional owners of Juukan Gorge, said they were “pretty upset” to discover Fortescue had applied for mining leases in the area after the PKKP had managed to secure a six-month moratorium from Rio Tinto on any further work in areas of high cultural sensitivity.

“We weren’t told by anyone that there was potential for FMG to come in from the side and actually apply for a mining licence,” said the PKKP Aboriginal Corporation chief executive, Carol Meredith.

Fortescue said it had held prospecting licences since 2012 over an area near Juukan Gorge. In the Australian, Gaines questioned the PKKP’s version of events, stating she had been “surprised and a little disappointed because we did advise them that we intended to convert that prospecting licence to a mining lease”.

Entsch said Fortescue had already lodged a written submission to the parliamentary inquiry but the new evidence had raised questions for the company to answer.

“As the Rio Tinto written evidence has shown, it was contested and proven to be less than accurate,” the chairman said.

“The inquiry is trying to get to the facts. This is an opportunity for FMG to put forward their facts. It would be very useful for them to give us their side of things, sooner rather than later, because the evidence we have heard over the past few days is quite damning.”

A spokesman for FMG said that from the outset Fortescue had intended to appear before the joint standing committee.

“Fortescue had previously confirmed arrangements for the committee to visit two Fortescue sites as part of the inquiry and for Fortescue to appear as part of that trip,” the spokesman said.

“This trip was unfortunately cancelled due to the closed West Australian border. Fortescue has been in regular contact with the committee secretary to find a suitable time to appear with appropriate notice. We look forward to the secretariat’s advice.”

The inquiry is planning to visit the Pilbara in early November.