A Northern Territory Government department retrospectively applied for approval to clear nearly three hectares of native vegetation in a conservation zone, even though the work was illegally already done in June.

The vegetation sat along an access road to the Dundee boat ramp, and was cleared without approval during upgrades, the Department of Infrastructure admitted.

The principal lawyer at the Northern Territory's Environmental Defender's Office said the breach set a poor example.

"If that's right it sends a very bad message to the community that the Government isn't taking small land clearing permit seriously enough to even go and get one for themselves," Mr Morris said.

The department said the clearing took place in June when the contractor engaged for the boat ramp's $4.5 million upgrades mobilised on site.

A department spokeswoman said it was agreed to undertake the clearing to provide construction access "in the interest of increased public safety", and to make more room to stockpile materials.

She said "unfortunately" development approval was not obtained.

"The clearing works were completed prior to [the department] becoming aware planning approval was required," the spokeswoman said in a statement.

"As soon as the department became aware that the clearing works required a permit, this was lodged."

Mr Morris said the Government should be setting the example in upholding the Territory's environmental regulations.

"There is a bit of a systemic problem with land clearing in the Northern Territory," he said.

"It's very common place for a land clearing to occur by a land owner and then for the department or the minister to issue a permit after the fact to regularise the land clearing that was on the face of it illegal.

"That's got to stop in the Northern Territory."

Last year the Development Consent Authority controversially dropped a case against a developer who illegally cleared four hectares of native vegetation on Boulter Road in Berrimah.

A spokeswoman for then planning minister Dave Tollner said the DCA was "unable to prepare a viable case" for prosecution, despite former planning minister Peter Chandler labelling it "a clear breach".