How 49 high-value Australian breeding cattle perished aboard a Boeing 747 flight from Melbourne to Almaty in Kazakhstan this week will be the focus of a new investigation by the Department of Agriculture, Fisheries and Forestry.

The dead cattle were discovered upon the plane's arrival in Almaty on Wednesday.

They were were part of a consignment of 321 cows air-freighted by Livestock Shipping Services to fill a Kazakhstan Government order for breeding cattle.

A mechanical breakdown affecting the plane's air conditioning system is believed to have left the 49 cattle without oxygen.

The Kazakhstan Government has imported 1592 breeding cattle from Australia since July last year under an initiative to strengthen the country’s livestock production and meat export capacity.

Kazakhstan has no sea port, and airfreight is the preferred method of transporting cattle to the country.

Exporter LSS said it had made five similar flights in the past five weeks without 'any problem in the world".

In a statement the Department of Agriculture, Fishieries and Forestry said it was investigating the reasons for the mortalities.

“As part of normal processes, the exporter advised the department that the reportable mortality level for cattle during the flight had been exceeded.

“The department is committed to a prompt and thorough investigation and to ensuring that it is as complete as possible and no shortcuts are taken.

"Further information about numbers and findings will be made public at the conclusion of the investigation.

"Reportable mortality events occur infrequently. Investigations into reportable mortality incidents are published on the department’s website.”

Kazakhstan media reported that the cattle were found dead after the aircraft landed in Almaty on Wednesday.

Tengrinews quoted the Chief Veterinary Inspector at Almaty, Omirserik Kydyrbatev, as saying the "infringement of rules of air transportation of animals" caused the deaths of the cattle.

A statement provided to local media by Kazgro, the agricultural arm of te Kazahstan Government, said: "The airplane carrying the live cargo arrived today during the night. But it was discovered that part of the cattle died along the way. At first the deaths were through (sic) to be caused by some virus. But later the Veterinarian Service of the Agricultural Ministry reported that they were caused by a failure in the air conditioning system of the airplane. All the expenses arising from the accident are going to be incurred by the supplying company, not by Kazakhstan."

Tengrinews said the animals were loaded into the plane in a bi-level configuration in special boxes.

"The animals on the lower level were fine, but those on the above level died. According to veterinarians, this happened because of the cows' natural wastes – ammonia became the source of poisonous vapors. And they suffocated because of insufficient supply of oxygen," one of the experts explained, according to the news outlet.

The plane made one stopover in Singapore for refueling.

LSS chief executive officer Gary Robinson told News Limited that he could not pre-empt the investigation but the mortalities were "very unusual".

"It's deeply worrying when you have an incident like this … we need to get to the bottom of it," Mr Robinson said.

Australian Livestock Exporters Council chief executive officer Alison Penfold said mortalities were uncommon on airfreight because the delivery time frames were very short.

“This is most likely a mechanical failure. Some people say the best way to not have a problem is not to airfeight, but that is like saying don’t drive a car if you don’t want to kill people," Ms Penfold said.

“The answer really is, how do you mitigate a risk of an accident happening, you drive more slowly and you follow the rules, you make sure your car is well serviced.

“It is the same with airfeight, there is a set of standards around air freight, there are checks to make sure things are functioning and some times things go wrong, and that is where we are with this unfortunately.”

WA livestock exporters association chairman John Edwards said the industry carried thousands of animals by air last year and with no mortality recorded.

For more information on DAFF's mortality invstigations  visit www.daff.gov.au/biosecurity/export/live-animals/livestock/aqis-mortality-investigations