Malakondaiah, currently managing director of AP State Road Transport Corporation, will take charge of his new assignment from Nanduri Sambasiva Rao, who is retiring tomorrow.
Malakondaiah will retire from service on June 30 next year.
The Union Ministry of Home Affairs had, last month, twice rejected a panel of names forwarded by the state for the DGP (HoPF) post.
The Centre rejected Malakondaiah's nomination twice as he had less than two years of service left and hence his appointment could be in violation of the Supreme Court's 2006 judgement in the Prakash Singh case.
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The ordinance also empowers the state government to choose the DGP (HoPF) on its own without having to send a panel of names to the UPSC.
The ordinance was issued even as the MHA approached the Supreme Court seeking clarity on the issue.
The state's contention was that as law and order is a state subject, the Centre or the UPSC could not have a say in the selection of the DGP.
The Government Order issued by Chief Secretary Dinesh Kumar said that M Malakondaiah is being appointed as DGP (HoPF) under section 3 of the Andhra Pradesh Police (Reforms) (Amendment) Ordinance, 2017.
Malakondaiah met Chief Minister N Chandrababu Naidu tonight and thanked him over the appointment, official sources said.