The programme will begin in Engineering but is open to other subject areas.
Some of the research areas identified for collaboration include computational modelling, cyber-security, and advanced materials, as well as precision-driven medicine and cancer research.
"The joint PhD programme significantly strengthens the economic and research ties between New Zealand and India. This historic agreement recognises the importance of top institutions engaging internationally," said Professor Stuart McCutcheon, Vice-Chancellor, University of Auckland in New Zealand.
"I welcome the opportunity this partnership will bring to enhance research outputs at both institutions, as well as the enriched learning it will deliver for PhD students," McCutcheon said.
Students from both Universites who participate in this programme will study under the supervision of academics in both institutions and will spend time in both universities.
Dr Caroline Daley, Dean of Graduate Studies at the University of Auckland, said doctoral candidates will have access to opportunities at both institutions, whether it's related to their research programme or their professional development.
"Employers are looking for doctoral graduates who can work in culturally diverse teams and who are able to adjust to new environments in a timely, positive way. Graduates of this joint PhD programme will have an excellent academic record, and a CV that stands out," Daley said.
Professor Sriman Kumar Bhattacharyya, IIT Kharagpur Director, visited the University of Auckland on Friday to officially sign the agreement.
"IIT Kharagpur - the first, the largest and the most diverse member of India's IIT Family - takes immense pride in initiating this joint PhD programme with New Zealand's top university," said Professor Sriman Kumar Bhattacharyya, Director, IIT Kharagpur.
"The scope of collaborations between the two institutions is vast and we will provide all necessary support to take our relationship to greater heights. I am looking forward to welcoming University of Auckland students and faculty into our campus at Kharagpur in the near future," Director Bhattacharyya said.
( With inputs from IANS )