The 36-year-old was demoted to the second-rung of players in the central contracts announced last week because of a rule preventing players who play in only one format of the game from being considered for a top level salary.
Khan, who is considered one of Pakistan's modern batting greats, is now seen as a Test specialist having played his last one-day international in 2013.
A Pakistan Cricket Board (PCB) statement said chairman Najam Sethi had intervened and proposed a change in the rules.
"The PCB chairman has taken notice of the rules relating to central contracts of players in which a renowned and star player like Younis has been placed in category "B", and ordered a suitable amendment to rectify the situation," the statement said.
"According to the new clause to be inserted into the rules, any player who has played over 300 matches in all three formats of the game, and has captained in all three formats will be placed in Category 'A'," it added.
Younus has so far played in 89 Tests, 253 one-day internationals and 25 Twenty20s, and led Pakistan to World Twenty20 title in England five years ago.
Revised central contract list:
Category A: Misbah-ul-Haq, Mohammad Hafeez, Saeed Ajmal, Shahid Afridi, Junaid Khan, Younis Khan
Category B: Ahmed Shehzad, Umar Akmal, Umar Gul
Category C: Asad Shafiq, Azhar Ali, Adnan Akmal, Khurram Manzoor, Nasir Jamshed, Abdul Rehman
Category D: Sohaib Maqsood, Sarfaraz Ahmed, Bilawal Bhatti, Sharjeel Khan, Zulfiqar Babar, Fawad Alam, Ehsan Adil, Mohammad Irfan, Wahab Riaz, Raza Hasan, Umar Amin, Haris Sohail, Rahat Ali, Shaan Masood, Mohammad Talha, Anwar Ali.
COMMENTS (4)
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He deserves to be included in category "A". I must say that He must be included in World Cup ODI squad also in first announcement. Pakistan Chairman Board oh sorry Pakistan Cricket Board must take right and wise decision timely and effectively.
Sethi is such a politician
Fawad Alam is in Category D???
What does Fawad have to do to get into Category A / B? Develop flying wings???
Can we do anything right in the first go??
Ahmad Shahzad should be 'A' Umar Akmal should be 'F'