External Affairs Minister S. Jaishankar and Human Resource Development Minister Ramesh Pokhriyal 'Nishank' jointly launched the programme here.
The fellowships could be taken up at the 23 Indian Institutes of Technology (IITs) across the country.
Officials said that with a total outlay of Rs 300 crore, the fellowship programme is touted to be the largest capacity development initiative by India in partnership with ASEAN. The fellowship will cover the full cost of study and living expenses for a duration of up to five years.
"Honoured to launch the largest capacity-building programme in the #ASEANIndia partnership - offering 1000 fellowships to the students from our SE Asian neighbourhood to carry out doctoral research at IITs. Thank Ministry of HRD @DrRPNishank & IIT for this initiative," tweeted Jaishankar.
IIT Delhi has been designated by the HRD ministry to coordinate for the fellowship programme that was launched at the External Affairs Ministry on Monday.
"To strengthen the deep and historical ties between India and ASEAN, India's foremost technical education centres, the internationally-renowned Indian Institutes of Technology (IITs), welcome scholars from ASEAN countries to apply for PhD fellowships. Applicants may apply online on our portal at http://asean.iitd.ac.in," the MEA said in a release.
It further said: "Those selected can complete their PhD with Government of India funding at par with Indian counterparts. Such funding will cover the entire cost of study and living expenses for up to five years of a PhD programme."
The ministry also added that in January 2018, Prime Minister Narendra Modi had announced India's offer to provide up to 1,000 integrated PhD fellowships for ASEAN students in IITs while attending the 25th Anniversary ASEAN-India Commemorative Summit in New Delhi.
The HRD Minister said that the ASEAN nations share deep cultural ties and this will be strengthened by this fellowship programme.
"The fellowships will strengthen our cultural, technical and financial relations. It will foster the three Cs culture, commerce and connectivity," he said.
( With inputs from IANS )