Silvia Alvarez, who directs the council's 'development of scientists' programme, had described the reductions as "nationalistic" as they favour Mexican research programmes over those abroad.
But CONACYT announced last week that it doesn't have enough funds to support about one-third of the 300 students, meaning the number of scholarships could drop to about 200.
The decision to cut scholarships contrasts with the Mexican government's 2001-2006 special programme of science and technology, which proposed as a main objective the production of more than 5,000 science doctorates each year.
Octavio Paredes, president of the AMC, disagrees, saying that the reduction in the number of scholarships threatens the development of high-quality human resources in Mexico. Mexican universities are inadequate and the students need to go overseas, he told SciDev.Net.
According to CONACYT, Mexico has only 25 postgraduate science programmes of 'international quality' and these are concentrated in just in two institutions in Mexico City: 12 are at the Advanced Studies and Research Centre, and 11 at UNAM.
Each year, only about 1,100 Mexicans are awarded PhDs, out of a population of over 100 million, and 60 per cent of these study in Mexico.
According with the Organisation for Economic Cooperation and Development (OECD), Mexico invests the least in science and technology of its 32 members, and is second to last in the number of doctorates awarded.