Panesar is going through an unsettled period in his private life and was fined by police earlier this month after urinating on bouncers at a Brighton night-spot he had been drinking in.
Sussex have since allowed him to leave the county, with Cook's own Essex side snapping the left-arm spinner up on a short-term deal.
Panesar's travails come less than a year since he was helping England to a series win in India and only a matter of weeks since he was an unused squad member in the third Ashes Test against Australia.
With Panesar not considered for duty for the series finale at the Kia Oval this week, England called on the uncapped Simon Kerrigan to provide back-up for Graeme Swann.
Panesar duly telephoned Cook to apologise and the pair discussed his future.
"Certainly what's happened over the last couple of weeks has been disappointing. I've spoken to him about it," said Cook. "He actually rang me up about it which shows he knows he's done wrong and has let the England shirt down a bit.
"It wasn't the most pleasant phone call he had to make, to ring the England captain to apologise. He recognises he needs a bit of a change in his life and this is the first step towards that.
"I didn't think his problems were as bad as that, (but) he's got to get that side of his life right because we all know how much a settled life can do for you."
Despite the excitement over Lancashire tweaker Kerrigan, Cook was unequivocal that Panesar had an England future.
"We all know the class he has as a bowler," Cook added.
"We have seen what he can do time and time again so he has to go back to the basics and does what he does best, taking wickets. If he does that, all the better for me.
"The bottom line is we need Monty bowling again the way we know he can bowl, as he did in India. The way back for him is wickets. We know the record he has in international cricket and we know his pedigree.
"We need to see him doing it again and hopefully he will be doing that at Essex.
"The door is certainly not shut on him but he knows what he has to do to get back."
- Sports & Recreation
- Simon Kerrigan