The June 3 meeting is scheduled against the backdrop of Jayalalithaa boycotting Modi's swearing-in ceremony on May 26 to protest Sri Lankan President Mahinda Rajapaksa's presence at the event. She had earlier dubbed as "unfortunate" the invitation to Rajapaksa.
Jayalalithaa will meet Modi at his South Block office, a state government release said, adding, she will present a memorandum to the Prime Minister.
"This memorandum will include some crucial issues relating to Tamil Nadu which have been pending with the Government of India," the release said, without elaborating.
Soon after she took over in 2011 following a strong mandate, Jayalalithaa had met the then Prime Minister Manmohan Singh to present a memorandum of various demands for the state, including a financial assistance package of Rs one lakh crore in the light of the state's debt situation.
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She had also raised the Sri Lankan Tamils issue, and pressed for demands including action against alleged war crimes.
While Modi had attended her swearing-in as Chief Minister in 2011, she had returned the favour by participating in Modi's swearing-in as Gujarat Chief Minister after he retained power in the 2012 Assembly elections.