KARACHI, PAKISTAN, June 7.-The Pakistani Government removed from circulation today part of the nation's currency in an effort to check the economic effects of looting from banks in East Pakistan.

The two largest denominations of Pakistani money, 500 and 100-rupee notes, worth respectively $106 and $21 at the legal rate of exchange, were recalled.

Also taken out of circulation were any other banknotes overprinted with the slogans of the Bengali separatist movement of East Pakistan.

President Agha Mohammad Yahya Khan said recently that $100 million in rupees had been taken from banks in East Pakistan by militant Bengali separatists in March and April .

Tonight the Government said this money, if it remains within the Pakistani economy, would be likely to have an inflationary effect. It asked that 500 and 100-rupee notes be turned in to Government banks for checking of serial numbers in the next three days.