The president, as advised by Prime Minister Narendra Modi, has accepted the resignation of Mr Raju and Mr Chowdary from the Union council of ministers with immediate effect, he said.
While Mr Raju was heading the Ministry of Civil Aviation, Mr Chowdary was Minister of State for Science and Technology and Earth Sciences.
"...the president has directed that the work of the Ministry of Civil Aviation will be looked after by the prime minister," the spokesman said.
Under relentless opposition attack over its failure to secure special category state status for Andhra Pradesh, the state's ruling TDP pulled out of the Modi government yesterday, but kept a window open for rapprochement by deciding to remain part of the NDA.
The two TDP ministers had met the prime minister last evening and handed over their resignation letters.