The ban imposed with immediate effect aimed at stockpiling the drugs in case of their possible use to treat Covid-19 patients, is set to remain in place until a further decision from Pakistan's Coordination Committee is announced, reported Dawn.
Additionally, there was a confusion between the Commerce ministry and Health ministry on who would allow the export or impose a ban on the export.
Hydroxychloroquine has been sought after by several countries after US President Donald Trump claimed it to be a "very powerful" drug and later the US Food and Drug Administration (FDA) approved the use of it in the treatment of COVID-19.
Meanwhile, India has stood strong with countries that have been worst hit by the coronavirus pandemic.
India on Friday cleared a list of 13 countries that will receive the anti-malarial drug HCQ and other active pharmaceutical ingredients (API).
As per the list, the USA, Spain, Germany, Bahrain, Brazil, Nepal, Bhutan, Sri Lanka, Afghstan, Maldives and Bangladesh, Dominican Republic and Seychelles will receive the medicine, the sources said.
USA had asked for 48 lakh tablets of HCQ and India has sanctioned 35.82 lakh tablets, sources said.
US President Donald Trump on Wednesday thanked Prime Minister Narendra Modi for allowing the export of HCQ. In a tweet he had also thanked India and the Indian people for the decision on HCQ, saying it will not be forgotten.
Israeli Prime Minister Benjamin Netanyahu and Brazilian President Jair Bolsonaro also thanked India for sending chloroquine.
( With inputs from ANI )