Gregan, who also came under heavy scrutiny after the Wallabies' northern hemisphere tour at the end of 2005, faces pressure to retain his number nine spot ahead of Queensland Reds star Sam Cordingley.
Cordingley has been ruled out of the next Tri-Nations clash with New Zealand with a foot injury but it has not stopped many observers calling for Gregan to be dropped.
Connolly accepts the Wallabies were below par in their scrappy 20-18 victory over South Africa last Saturday, but does not feel his veteran skipper should be targeted.
"We said all along that we will review everything after the Tri-Nations but at the moment, the least of our problems is George Gregan," Connolly told ABC Sport.
"I think he's played pretty well and I can't agree with the criticism that is levelled at him. I think it is quite unfair."
With Cordingley ruled out, Connolly has called up uncapped NSW Waratahs pair Brett Sheehan and Josh Holmes as the possible replacements, but has played down suggestions inside centre Matt Giteau will also come into the equation.
"Brett Sheehan and Josh Holmes will come down and I guess we have three options there as George's back-up," he said.
"We can use Giteau as a back-up but that's a concern as he hasn't put a ball in a scrum or taken a ball off a line-out in four years as a half-back."