Announcing his appointment, the External Affairs Ministry said Kwatra is expected to take up his assignment shortly.
A 1988-batch foreign service officer, Kwatra will succeed Mohan Kumar, who is retiring.
Apart from having experience of dealing with the UN organisations such as International Labour Organisation (ILO) and World Health Organisation (WHO), he has served in Indian diplomatic missions in China and the US.
He has also held the position of joint secretary incharge of the counter-terrorism division in the MEA.