Heptulla, who had crossed 75 years, resigned today from the Union Cabinet along with Minister of State for Heavy Industries G M Siddeshwara.
Announcing their resignations, a Rashtrapati Bhawan communique said these have been accepted.
There was speculation last week when Prime Minister Narendra Modi undertook the reshuffle that Heptulla and Minister of Small and Medium Enterprises Kalraj Mishra, who had recently turned 75, could be asked to quit.
The Rashtrapati Bhawan communique said Mukhtar Abbas
Naqvi, who was Heptulla's deputy, has been assigned the Independent charge of the Ministry of Minority Affairs.
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According to government sources, Heptulla (76) was out of country and therefore could not submit her resignation on July 5 though she had decided to do so.
Siddeshwara, a Lok Sabha member from Karnataka, is believed to be among those who were asked to resign in the reshuffle on July 5 but he, sources said, had sought more time due to his birthday on the same day.
Babul Supriyo has been relieved of his existing portfolios as Minister of State for Urban Development and also Housing and Urban Poverty Alleviation.
While Heptulla has resigned, Mishra remains in the Cabinet despite crossing 75 years. It is believed that he has been retained considering the crucial Uttar Pradesh Assembly polls early next year as he is noted Brahmin leader from the state.
Five ministers of state, Nihalchand, Ram Shankar Katheria, Sanwar Lal Jat, Manuskhbhai D Vasva and M K Kundariya were dropped in the reshuffle.