A letter from Labor's regional communications spokesman Stephen Jones has asked that the decision to place the tower on the Kingstown property be scrutinised.

"I believe the decision-making around the location of this particular base station should be investigated to ascertain if proper departmental procedures were adhered to and if decision-making was influenced by factors outside of the program objectives," Mr Jones wrote.

"I understand that you are already considering an audit of Round 3 of this program.

"In that round, the Coalition Government selected the locations for co-funding, leading to criticisms from state governments alleging the program was not delivering good outcomes for the community."

Kingstown residents have complained that the tower has been plagued by reception problems since it was switched on two weeks ago.

Member for New England Barnaby Joyce campaigned for the tower and announced it as part of the federal government's Mobile Black Spot program in June 2015.

He said he had no say in the exact location of the phone tower in Kingstown.

Mr Joyce told The Inverell Times on Tuesday afternoon that the referral of the issue to the auditor-general was a political stunt.

"The Labor Party of course will play games, this is a political tactic," he said.

"I could refer anything; I could refer Mr Jones if I wanted too."

Mr Joyce said he worked to get the funding for the tower in the village, but where it is placed is up to Telstra.

He rejected any assertion he had any dealings with Gina Rinehart on the issue, and said the government and Telstra negotiated with the previous owners of the property, prior to her purchase

"I have never have had any conversation with Ms Rinehart with any purchase of hers in the New England," Mr Joyce said.

"Any negotiations about the phone tower do not include me; I provide the money for a phone tower in Kingstown, it's up to Telstra where it puts it.

"If it was up to me, I would have put it on top of the hill so that it gives coverage to the whole town."

The tower is located on Sundown Valley, a property purchased by Gina Rinehart's pastoral arm, Hancock Agriculture, in August last year.

But the contract with Telstra to host the tower was signed by the previous owners, Hancock Agriculture chief executive David Larkin told the Times, and said the annual rent paid on the tower was not a motivation.

The Australian National Audit Office (ANAO) will now consider the request, a spokesman for the Auditor-General said.

"As outlined in the ANAO corporate plan, the Auditor-General aims to respond to the vast majority, 90 per cent, of requests for audit within 28 days," he said.

It's not the first time the federal government's Mobile Black Spot program has been referred to the national audit body.

READ MORE: Third drought assistance package announced

A 2016 ANAO investigation found the $110 million program did not target the funding to areas where coverage had not previously existed. 

At least 89 of the 499 base stations provided minimal new coverage at a cost of $28 million; that means the public funded a program that did not extend coverage into new areas.

The investigation also found that there was not a structured method for assessing the technical and financial aspects of proposals.

It found that the department's ability to measure the effectiveness of the program was difficult, given there was no way to evaluate it.