"I am disappointed that, if these numbers of livestock have died, that that occurred. But...from time to time, livestock do die," Mr Guy told reporters.
The sheep were not on pasture but under some shelter, he said. Asked how so many lambs could die if there was shelter, Mr Guy said there "was a lot of sand in the desert".
"There is a lot of sand and the wind can get up and that caused, as I understand it, some mortality. But I don't have all of the information. Because MPI's role is about the transportation of stock, and adhering to the animal welfare conditions."
Labour's primary industries spokesman Damien O'Connor went on the attack over the Saudi farm deal, which cost taxpayers a total of about $11.5 million, during this morning's select committee.
He queried why money was spent on the farm to act as a demonstration model for New Zealand agribusiness, given it was in a desert, and asked for a full inquiry into MPI's role in the process. That request was declined by Mr Guy.
National has come under intense pressure over the deal, which was done partly to resolve a dispute and clear the way for a regional free trade deal.
Foreign Minister Murray McCully has blamed the previous Labour Government for antagonising Mr Al Khalaf to the point he took advice that he could sue for $30 million.
Mr Al Khalaf lost millions of dollars when a ban on the export of live sheep for slaughter was implemented under the previous Labour Government, and then subsequently extended by National.
The farm deal was a way to defuse that risk, set-up a farm to showcase New Zealand agribusiness, and clear away ill-feeling from the Saudis so that a regional free trade deal could progress, Mr McCully argued.
That version of events has been strongly rejected by Labour, who say National is attempting to shift the blame for actions that would be labelled bribery in many other countries.
Labour's trade spokesman David Parker released redacted 2007 Cabinet papers yesterday that showed that, while Labour was aware of the displeasure a ban would cause Mr Al Khalaf and the Saudis after earlier negotiations had indicated the halt on exports would be overturned, there was no reference to possible legal action from a private investor.