The 26-year-old England international was expected to complete a move to west London as soon as the transfer window reopened, after the two parties agreed a fee believed to be in the region of £5million.
However, last week the Blues boss suggested that Cahill's arrival at Stamford Bridge was far from a full-gone conclusion.
Villas-Boas suggested that after preliminary contract negotiations the club and the defender's representatives were 'miles apart' regarding an agreement.
Speaking after Chelsea's 2-1 victory over Wolves on Monday, he added: "It's an ongoing process. I never thought it would be solved quickly."
Cahill is entering the final six months of his Trotters contract, and if no agreement is reached then he could leave the Reebok Stadium for free at the end of the season.
Meanwhile, Cahill's central defensive partner Zat Knight, feels that the move to Chelsea will enable him to become a regular in Fabio Capello's national team.
"When you play with top players it brings the best out of you," he said. "He's a fantastic player but hopefully there's a lot more for him still to give.
"He's shown in the last few seasons how good he is. Now if he's going to be playing week in, week out with John Terry and Ashley Cole then he'll get a lot more games with England."
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