"There have been instances when the authentication details of certain class of e-filers have been obtained by persons from sources other than the website and then the passwords were reset and the e-filing account accessed," the ministry said.
As many as 2.96 crore have filed income tax returns online during 2013-14.
Replying to an RTI query, the ministry said a process of "multifunctional authentication" has been designed and will be in place shortly to address any illegal access to e-filers' accounts.
The ministry was asked to give details on hacking of income tax returns filing accounts of individuals and measures being taken by it to check such activities.
Mumbai Police had late last year claimed that e-filing accounts of top industrialists, actors and cricketers including Anil Ambani, Sachin Tendulkar, MS Dhoni, Shah Rukh Khan and Salman Khan among others were unauthorisedly accessed.
"There are mobile applications which are not approved by the Income Tax department. Users are advised that they may not be according to Department Data Structure. Filers using them are doing at their own risk," said a warning on the income tax department's website for e-filing.