South Africa withdrew on safety grounds after a bomb blast in Karachi last Friday, but at a Cricket South Africa meeting on Tuesday it was agreed in principle to go ahead after changes to the schedule dropped Karachi and Peshawar.
However, Mani said on Tuesday he was worried there had been an apparent lack of consultation between the relevant bodies before the original decision was reached.
"Clearly safety and security is the over-riding consideration for any board and each board must have the final say on where and when its team plays," he said in an ICC statement.
"In this instance, though, I am concerned that there appeared to be a lack of consultation within the international cricket community before the initial decision not to tour was taken.
"This meant that both the ICC and the Pakistan Cricket Board were not given the opportunity to provide relevant information to the UCB as it considered its position."
Mani said one solution could be to introduce a standard protocol for similar situations whereby the touring country would be obliged to consult with the ICC and the host country before reaching a decision.
"In that way every country would retain its right to determine where and when its team plays but it would also ensure that all parties affected by its decisions would be able to have their views considered and discussed," Mani said.
But the president praised the way that the PCB and UCB had worked together to revive the tour.
"Since the decision not to proceed with the tour was first announced the ICC, the PCB and the UCB have been in constant discussions," said Mani.
"I am very pleased that through this process the PCB and the UCB have reached this in principle agreement."
The new tour, from October 1-28, is expected to consist of two Tests and five one-dayers.
