Former Australia captain John Eales backed up these complaints with his own criticism after the Wallabies' narrow defeat in Brisbane last week.
But Jones, who played 105 games for the All Blacks, expects Henry and forward specialist Hansen to solve the problem.
He told The New Zealand Herald: "Graham Henry and Steve Hansen have got everything else right and I'm sure they're going to get this right. I have a lot of faith in them.
"You can do thousands of line-outs in practice but the only place you are going to find out what works is in games and against opponents who are really after you. I suspect they may even have known this problem would arise.
"Keven Mealamu and Andrew Hore's throwing techniques look as good as any in the world. We have the lifters and jumpers. All the bits are there.
"Maybe it is as simple as combinations. A lifter such as Rodney So'oialo must instinctively know what Ali Williams is going to do, and how he does it. If you have to think, then the moment is lost."
The All Blacks return to action against Australia in Auckland in two weeks' time.