Department of Premier and Cabinet secretary Chris Eccles quit on Monday after his phone records were handed to the hotel quarantine inquiry at the weekend.

In a statement, Mr Eccles admitted the records show he spoke to former Victoria Police chief commissioner Graham Ashton at 1.17pm on March 27, the day it was decided private security guards would staff quarantine hotels.

"The telephone records do not in any way demonstrate that I, or indeed anyone else in DPC made a decision that private security be used in the hotel quarantine program," Mr Eccles said.

"I am absolutely certain I did not convey to Mr Ashton any decision regarding the use of private security as I was unaware any such decision had been made, and I most certainly had not made such a decision myself."

Mr Eccles had told the inquiry he did not recall speaking to Mr Ashton at that time.

Premier Daniel Andrews told reporters on Monday he was "shocked" when he learnt Mr Eccles had made the call.

"I believe he has made the right choice (to resign)," he said.

"It was not a matter of me having to instruct him, he said his position was not tenable. I did not need to urge him."

Mr Andrews said deputy secretary Jeremi Moule has been appointed acting secretary.

The two-minute phone call between Mr Ashton and Mr Eccles occurred in a critical six-minute window when, according to the former police chief's messages tendered to the inquiry, the decision to use guards was made.

"Mate. Question. Why wouldn't AFP Guard people At The hotel??" Mr Ashton wrote to the Australian Federal Police Commissioner Reece Kershaw at 1.12pm on March 27.

At 1.16pm, Mr Ashton also messaged Mr Eccles: "Chris I am getting word from Canberra for a plan whereby arrivals from overseas are to be subjected to enforced isolation from tomorrow. The suggestion is Victorian arrivals are conveyed to a hotel Somewhere where they are guarded by police for 14 days. Are you aware of anything in this regard?? Graham".

The phone records reveal Mr Eccles called Mr Ashton a minute after receiving his message.

Six minutes later, at 1.22pm, Mr Ashton sent another message to Mr Kershaw: "Mate. My advise (sic) is the ADF do passenger transfer and private security will be used."

"Ok that's new," Mr Kershaw replied.

"I think that's the deal set up by our DPC," Mr Ashton said.

Mr Eccles, who has previously held similar roles in NSW and SA under Labor and Liberal-led governments, said it would be a "distraction" if he remained.

"I do not want a focus on me to in any way undermine the extraordinary work of the public sector as it continues to respond to unprecedented challenges of 2020."

The decision to use private security guards in the program is believed to be responsible for the state's second devastating wave of coronavirus, which has killed hundreds of people and led to the nation's toughest lockdown.

Health Minister Jenny Mikakos resigned last month over her department's role in the program.

In her response to the inquiry's closing submissions, Ms Mikakos said it was "implausible" to suggest no one made the decision to use private security guards.

The inquiry, led by retired judge Jennifer Coate, is due to hand down its final report on November 6.

Australian Associated Press