India were at the receiving end of at least five contentious calls in the first two Tests, both of which the visitors lost, prompting Dhoni to state that umpiring could certainly improve.
But Lyon defended the officials, saying, "I personally think they've done a pretty good job."
"I know it's been quite tough for them, especially in Adelaide. That wicket was a pretty tough wicket. They've made some big decisions. Some have gone against India, some have gone against Australia.
Lyon called on both the teams to keep their emotions in check during the third Test starting Friday after tempers flared up during the second Test in Brisbane.
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Lyon, however, refuted suggestions that absence of the controversial Decision Review System contributed to the tensions due to umpiring bloopers.
"It's going to swing both ways. We could have had a different result in Adelaide (in the first Test) if we had DRS but in saying that it could have went our way again. Both teams have to agree to use it.
Lyon said a couple of bad umpiring calls should not be a provocation for on-field spats.
"You're going to have to control your emotions out there. We know in Adelaide some emotions were flying quite high when a couple of decisions weren't going either way," he said.
"But that's Test match cricket. There's enough emotions out there in the middle. We just have to keep patient and keep working hard and not worry about what the umpire says," he added.