Mushtaq and Naved are prolific wicket-takers in English cricket
The Pakistan Cricket Board says it cannot prevent non-contracted players from appearing for English counties.
The board has given Mushtaq Ahmed and Rana Naved 'no objection certificates' to enable Sussex and Yorkshire to register them for the 2008 season.
But the Board of Control for Cricket in India wants them excluded for playing in the unsanctioned Indian Cricket League competition.
The BCCI is now planning a protest to the England and Wales Cricket Board.
"We have an understanding with the other countries' boards that they can't allow players who are associated with the ICL to be allowed to play at any level.
"If the news is true that the two players have been given NOCs by the PCB, then we will take the matter up with the ECB, since the two counties come under the jurisdiction of the England board," BCCI secretary Niranjan Shah told the cricinfo website.
The England and Wales Cricket Board has refused to register five players who have appeared in the ICL - South Africans Andrew Hall, Johan van der Wath and Justin Kemp, New Zealander Hamish Marshall and Wavell Hinds of the West Indies - for the new county season, which starts next month.
But with NOCs in place, there is nothing to stop Mushtaq and Naved from fulfilling contracts with their respective English clubs.
The PCB's chief operating officer, Shafqat Naghmi, said they had a clear policy preventing ICL players from appearing in Pakistan cricket at any level.
But he added: "If they go and play county of shield cricket, we can't stop them.
"We have no legal or moral reason to stop ICL players from playing in any event, in any country, apart from Pakistan.
"If anyone in any other country wants to play them, it is their decision."
We cannot afford to wait a month and then have to find an overseas player
Sussex chief executive Gus Mackay
India's stance, meanwhile, could result in Sussex and Yorkshire being barred from a Champions League competition due to be staged in India in October, which will feature the leading Twenty20 teams from India, England, Australia and South Africa.
Sussex chief executive Gus Mackay said, however, that they had not seen any formal plans for the tournament and could not afford to delay finalising their squad for the summer.
"There has been so much speculation about this champions' competition and we are none the wiser.
"We cannot afford to wait a month and then have to find an overseas player; there has been an indication this tournament will take place but we have seen no tournament arrangements."