Khan, who was deputy to former skipper Inzamam-ul-Haq for nearly two years, is demanding full powers like his powerful predecessor, a condition unacceptable to the Pakistan Cricket Board (PCB), board sources said.
Following the country's humiliating first round exit from the World Cup in Caribbean the PCB says it wants to put in place a new code for players and the captain.
"The new strategy envisages strong checks and balances on the captain to curtail his role in selecting players and dictating terms to the coach and the management, as has been the practice in the past," a PCB official told AFP.
"Younis Khan wanted to be an all-powerful captain and is reluctant to accept curbs," the official said on condition of anonymity.
The PCB wants to curtail "player power", which it believes has been responsible for the poor showing of the national team in big tournaments.
The official said announcement of the captain had been delayed as the PCB authorities try to resolve the problem.
However a PCB spokesman said the delay in choice of men for the two key posts was not due to any differences with Khan.
"The board is still discussing various options on who should be appointed as captain and coach for the team," spokesman Ahsan Malik told AFP.
"We have not reached the stage where we can offer captaincy to any player, we have chalked out a criterion and once that is settled we will announce the name."
Khan was appointed as Pakistan captain for the Champions Trophy in India in October when Inzamam was banned for bringing the game into disrepute during the Oval Test controversy last year.
But Khan initially refused the role at the time, saying he did not want to be a "dummy captain", apparently over differences with some of the senior players and over some selections.