Khan said that the Indian cricket board officials had told him clearly that they had no role to play in Pakistani players not taking part in the IPL since 2009.
"The Indian board has said that the franchises want to have Pakistani players - crowd pullers like Shahid Afridi but they don't for fear of security," he told reporters here.
"The concern of the franchises is that the majority of the crowds in India are not favorable to Pakistani players and they fear security issues if Pakistani players take part in the IPL," he said.
"Ties between the Pakistan and Indian cricket boards have always been cordial even during tense diplomatic and political ties and we hope it continues that way. But what has happened in hockey and kabbadi is unfortunate and could have been avoided," he said.
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Khan said the relations between the two countries couldn't afford such skirmishes and disputes in any sports.
"What happens is this leads to negative reactions from Indian crowds and media and that is why I don't see our players in the IPL very soon," he said.
"Frankly speaking everything will depend on the situation of ties between both countries than. So we can only hope that the first series of this bilateral agreement goes ahead next year," he said.
Khan said the PCB was counting on the series when it hosts India at a neutral venue to improve its financial health.