"I also made it clear to him that the path he adopted was not right as a senior player," he said on the Cricket Baaz channel on YouTube.
"I think Amir is a valuable player for us even now and we will now make efforts to bring about rapprochement between him and the coaches."
Babar Azam had recently said he is ready to speak to Amir about his issues and Khan said once that discussion takes place, the PCB will bring the two parties to a table and try to sort the matter out.
Khan, however, was not able to give a deadline when Amir could be back in the Pakistan team when asked if he would be available for the World T20 this year.
Amir, 29, had announced his retirement from international cricket last December due to his differences with the coaching duo of Misbah-ul-Haq and Waqar Younis.
Amir had insisted that Misbah and bowling coach Waqar have not been fair with him and he will not make himself available for selection until they are in charge.
The left-arm pacer has signed a contract to play in the Caribbean Premier League for Barbados. He will also be seen in action in the Pakistan Super League matches in Abu Dhabi from June 9 for the Karachi Kings team.
Khan said Amir's issue was a complicated one but can be resolved.
He also made it clear that the PCB had no grievances with out-of favor batsman Umar Akmal, who completed a 12-month ban for not reporting spot-fixing approaches made last year and also paid a fine of 4.2 million rupees to the board.
"In fact I have just completed the 2 month rehabilitation program for Umar with our Anti-Corruption department and Umar can start the rehab soon," Khan said.
"He is a Pakistan player and we wish him well and he can resume his cricket career soon."
The PCB CEO said the board has advertised for the post of a sports psychologist to address the communication problems of some players, who sometimes go overboard with their grievances in the social media.