Choubey, a 1981-batch IAS officer of Tamil Nadu cadre, took over the charge from V Somasundaran.
He is the third Civil Aviation Seceratry at Rajiv Gandhi Bhawan after the formation of the BJP-led NDA government at the Centre in May last year.
Choubey took charge at the Ministry this morning, Ministry officials said.
Prior to becoming the Civil Aviation Secretary, Choubey was Additional Secretary in the Power Ministry.
Somasundaran, a 1979-batch Kerala cadre IAS officer, who had joined the Civil Aviation ministry last September has been shifted to the Ministry of Women and Child Development as its Seceratry.