Ali was able to provide support for the development of ornithology in India by identifying important areas where funding could be obtained. He helped in the establishment of an economic ornithology unit within the Indian Council for Agricultural Research in the mid-1960s although he failed to gain support for a similar proposal in 1935. He was also able to obtain funding for migration studies through a project to study the Kyasanur forest disease, an arthropod-borne virus that appeared to have similarities to a Siberian tick-borne disease. This project partly funded by the PL 480 grants of the USA however ran into political difficulties with allegations made on CIA involvement. The funding for the early bird migration studies actually came for the early studies from the US Army Medical Research Laboratory in Bangkok under the SEATO (South Atlantic Security Pact) and headed by H. Elliott McClure. An Indian science reporter wrote in a local newspaper that the collaboration was secretly exploring the use of migratory birds for spreading deadly viruses and microbes into enemy territories. India was then a non-aligned country and the news led to political upheaval and a committee was set up to examine the research and allegations. Once cleared of these allegations, the project however stopped routing the funds through Bangkok to avoid further suspicions and was directly funded by the Americans to India. In the late 1980s, Ali also headed a BNHS project to reduce bird hits at Indian airfields. He also attempted a citizen science project to study house sparrows in 1963 through Indian birdwatchers subscribed to the "Newsletter for Birdwatchers".