The comments come amid stinging criticism from India's former leader over Modi's alleged mishandling of the issue, following a string of particularly brutal rape cases which shocked the nation and triggered nationwide protests.
Modi, who is currently visiting the UK, made the remarks during an address to selected members of the Indian-diaspora in London.
Around 100 sexual assaults are reported to police in India every day, according to the National Crime Records Bureau.
There were nearly 39,000 alleged attacks in 2016, an increase of 12% on the previous year.
"Any time a small girl is sexually assaulted, it is painful for all us," Modi said in London.
"But can we compare the number of rapes in different governments? We can't say there were this many rapes in our government and that many in yours. There cannot be a worse way to deal with this issue," he added.
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Fallout from recent cases, including two alleged unrelated attacks on girls aged 16 and eight, is threatening to overshadow Modi's visit to the UK.
On Wednesday, hundreds of protesters gathered outside Downing Street and the British Parliament, waving placards reading "go home Modi" and "hang the rapists" as the premier prepared to meet his British counterpart Theresa May.
The article originally appeared on CNN