In an interview to Geo Super in Abu Dhabi, Whatmore said, "I think this (language barrier) was an issue specially the part where the communication came back."
Many former Pakistani players had criticised the decision of the cricket board to appoint a foreigner as a coach, pointing out that the language barrier was always a big impendiment between the coach and the players.
The former Australian player, who has also coached the Sri Lankan and Bangladesh teams, said he got a feeling that some players found it difficult communicating back to him.
"Obviously, there is a feeling when you are getting ready to leave a bunch of players you have been with for two years but I am happy that the Pakistan cricket board and I am parting ways on a good and cordial note," he said.
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"I am happy with the way things have worked out with the board and, in future, if there is an opportunity to come and work in some other capacity with Pakistan cricket, I will do it," he added.
Whatmore said he was looking forward to spending quality time with his family.
Whatmore said 2013 had been a tough year for Pakistan cricket but the team came back strongly in South Africa where it won the one-day series.