The ultimate source(s) of the numbers can be easily found in the Wikipedia article (which is well referenced):
A doctor at a rehabilitation centre in Dhaka reported 170,000 abortions of pregnancies caused by the rapes, and the births of 30,000 war babies during the first three months of 1972. Dr. Geoffrey Davis, an Australian doctor and abortion specialist who worked for the programme, estimated that there had been about 5,000 cases of self-induced abortions. He also said that during his work he heard of numerous infanticides and suicides by victims. His estimate of the total number of rape victims was 400,000, twice as high as the official estimate of 200,000 cited by the Bangladeshi government.
There were apparently enough Western academics trusting these numbers. On the other hand, the official Pakistani position still seems to be that the rapes only "numbered in the hundreds" (according to the the Wikipedia page).
These numbers are not official or the subject of a rigorous investigation. The number of Birangonas listed by name in official records (following a 2014 High Court decision to recognized them as freedom fighters) has reached 185 as of June last year (the most recent article I could find). So there is indeed a very large gap [at the moment] between individually accounted for victims and initial/rough estimates.