The goal of the campaign was to immunize 33.5 million children under five years of age, reports The Express Tribune.
A report compiled by the Polio Operation Room revealed that the campaign, hindered by varying factors in each province, fell short of its aims.
Out of the 1.3 million children, 809,225 were from Punjab - the highest figure from amongst all administrative divisions of the country.
A total of 278,210 children went unvaccinated in Sindh; 173,111 in Khyber-Pakhtunkhwa; 37,016 in Balochistan; 31,048 in the Federally Administered Tribal Areas; 10,513 in Islamabad and 833 in Gilgit-Baltistan.
However, Dr Altaf Boson, national coordinator for monitoring Pakistan's polio vaccination programme termed the first national anti-polio campaign of 2013 a success as no untoward incident took place. He said the figures of the missed children cannot be considered as final because the polio cell is still waiting to receive statistics from all over the country.
The last national anti-polio campaign held in October 2012 missed around one million children, including the 45,000 children whose guardians refused to allow for the vaccination. Later in March, during a sub-national immunisation drive, around 500,000 children were missed.