It also said it was concerned at a "lack of clarity" about the project's wider economic benefits, outside of royalties and taxes.
TTR appealed the July decision, but yesterday advised the High Court it was withdrawing the challenge.
A statement from chief executive Tim Crossley said the company still believed the grounds for appeal were strong.
However, it had been advised that it was "highly improbable, if not impossible" to reconvene within a reasonable timeframe the EPA-appointed decision making committee (DMC) that heard the application.
"Therefore, the prime remedy TTR was seeking through the appeal, which was to have the original marine consent decision set aside, have the court order the EPA reconvene the DMC to rehear the application correctly under the direction of the High Court, has little value as the outcome will still entail a new hearing," the company said.
"Such an outcome provides little or no advantage to TTR over that of submitting a new marine consent application.
"Given this outcome Trans-Tasman Resource's Board is considering its options including submitting a fresh new marine consent application."
The group Kiwis Against Seabed Mining, which fiercely opposed the bid, which it called "dodgy" and "shonky", said the appeal withdrawal should be "a blow" to the wider seabed mining industry.
"This should send a strong message to the Government and to investors that seabed mining is the wrong horse to back," spokesperson Phil McCabe said.
"It is now time that they considered our call for a moratorium on seabed mining in New Zealand waters."
Also responding to the development, the Environmental Defence Society said the groundwork that was necessary to justify approval for the project "just hadn't been done".
Chairman Gary Taylor said the organisation was not opposed in principle to sand-mining, provided it could be done responsibly and without significant harm to the marine environment.
"So we think that the company has made the right decision and we will follow its progression towards a fresh consent application with interest.
"At this stage our advice - for what it's worth - would be not to rush it: the job ahead will require careful scoping and implementation and leave no gaps.
"Having sound baseline information and a full understanding of the environmental impacts is an essential pre-requisite for approvals under the new EEZ Act."