Victoria's Chief Health Officer Brett Sutton has been ordered to explain discrepancies in his evidence to the hotel quarantine inquiry, as new evidence threatens to "unsettle" the November 6 deadline for the final report into the botched program.

In an extraordinary special hearing on Tuesday, counsel assisting Tony Neal, QC, said both past and new witnesses to the inquiry may be required to give fresh statements after "two discrete developments" raised further questions over the fateful decision to hire private security guards in the program.