In a letter to Modi, the text of which was released to the media here, he requested the removal of design flaws in the Udaan scheme of the Central Board of Secondary Education (CBSE).
He also urged the government to extend the last date for applications for the programme to at least Nov 30, 2014.
The CBSE has launched Udaan to mentor girl students to compete for admission to premier engineering colleges, including Indian Institutes of Technology (IITs) and National Institutes of Technology (NITs).
Under the scheme, 1,000 girl students studying in class XI and XII under all boards of education are to be selected on merit for receiving special online and direct coaching for entering into IITs and NITs.
Out of the total 151 contact class centres listed for the country, only two are listed in Tamil Nadu and none in Chennai, Panneerselvam said.
"On the other hand, a much larger number of centres have been provided in many other states. Two centres in a large state with substantial girl student population in the science stream is very inadequate and this by itself would act as a dampener for participation by girl students," he said.