David Littleproud says he has no power to intervene in a move by Emanuel Exports to ship live sheep to the Middle East under another name, two weeks after the company’s primary licence was suspended pending an animal welfare investigation.

Fairfax Media has reported that the Perth-based company applied to the federal department of agriculture to use one of its two remaining active export licences to deliver the consignment of 60,000 sheep to a buyer in Kuwait.

The federal agriculture minister, who has said that he wanted to target rogue exporters, said in a statement on Tuesday that “all decisions on live export licencing, issuing of export permits and related matters are made by the independent regulator alone.

“I have no power to interfere in the operations of the independent regulator. I have official advice from the regulator confirming I have no power in these matters.”

The department confirmed it had been “notified of” and was considering an exporter’s intention to export live sheep to the Middle East.

The sheep have been held in a feedlot outside Perth since the federal department suspended one of the company’s three export licences on 22 June.

The licence was suspended as part of an investigation into leaked footage aboard the Emanuel Exports stocked ship Awassi Express, including a voyage to the Middle East in August last year where more than 2,400 sheep died from heat stress.

Emanuel Exports has consistently maintained that it intends to follow through on its plan to export the sheep, despite the licence suspension and an offer by abattoir Fletcher International Exports, brokered by the WA government, to slaughter the sheep locally and then export the meat.

Initial suggestions were that it would work with another live export company and use their licence, but it now appears Emanuel, which is Australia’s largest live sheep exporter, will rely on a licence held by a related company.

EMS Rural Exports Pty Ltd is a wholly owned subsidiary of Emanuel Exports, headquartered at the same West Perth address.

On 29 June, the Australian Investments and Security Council registers for both Emanuel Exports and EMS Rural Exports were updated to withdraw the directorship of 70-year-old Graham Daws and appoint his son, Nicholas, as director and company secretary.

Under Australian export rules, if an export licence is disqualified, other licences held by the same person are also rendered inoperable. In withdrawing as a director, Graham Daws has also effectively withdrawn as a licence holder.

Emanuel Exports has declined to comment while negotiating its licencing arrangements with the department.

The Australian Live Export Council (Alec), which represents Emanuel, said negotiations with the regulator were continuing.

The Kuwait flagged livestock carrier Al Shuwaikh has been in WA waters since late June awaiting export approval and was moved into port in Fremantle on Monday.

“The sheep, mostly young Merino wethers, are booked to be exported on the livestock vessel, the Al Shuwaikh, to Kuwait and parties involved in this consignment are committed to transporting the sheep as soon as possible,” Alec said.

The department said all export applications were considered on their merits and in accordance with legislation.

Animals Australia said it would consider legal action if Emanuel used one of its sister licences.

“The department has the power to suspend the licences of all related companies,” spokeswoman Lyn White said. “The public would quite rightfully expect nothing less in the circumstances.”

Exporters have been under increasing pressure since April. In May they were forced to increase the space allowance and put independent observers on board ships to the Middle East, following an animal welfare review.

Littleproud also ordered a second review into the culture and investigative capabilities of the department, due next month.

Labor says it will phase out the live sheep trade if it wins government.