However, he said he was still optimistic the deal would be completed and that Cahill would join Chelsea after the January transfer window opens on Sunday.
Bolton manager Owen Coyle, speaking before Saturday's Premier League match against Wolverhampton Wanderers, earlier told reporters: "There has been a fee agreed between the clubs and we have now given Gary's representatives permission to speak to Chelsea.
"That is where we are with it. We obviously have a game tomorrow and I have said to Gary that he has to be focused on giving everything for Bolton Wanderers, because he knows Bolton Wanderers has been terrific for him just as much as Gary has been for us.
"That is why they have representatives - to sort that out - and whatever January 1 brings, it will bring."
Villas-Boas said there was plenty of negotiating still to be done.
"I would like to say we are miles apart regarding an agreement with the player so we will continue to monitor this situation as we are continuing to monitor the other targets that we have outlined," he said.
"But I think we can sort out [a deal] I think so," he added.
The 26-year-old Cahill, who has played seven times for his country, will link up in the middle of the Chelsea defence with England skipper John Terry and effectively replace Alex who is expected to return to Brazil next month.
Cahill joined Bolton from Aston Villa in 2008 and has developed into an outstanding defender even though his team have struggled all season and are 19th in the 20-team league.
He is out of contract at the end of the season and was linked with a move away from the Reebok Stadium last summer with both Manchester United and Tottenham Hotspur reported to be interested.
Chelsea now look poised to sign him for a fee of around 7 million pounds, according to media reports.
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