"Ronaldo is the best player in the world but still we should have a statue of a football player from Goa," Fernandes told AFP.
Michael Lobo, a local minister with India's ruling Bharatiya Janata Party, told AFP the aim was to inspire young people to excel not just inside the country but internationally.
"All the boys and girls who want to make football a career will get inspired by people like Cristiano Ronaldo," Lobo said.
"If you pursue your dream and you're passionate about it then you can reach a higher goal. This is what we have written on the plaque."
Most of present-day India gained independence in 1947.
But Portugal's then military dictatorship only relinquished Goa following an invasion by the Indian army and a two-day war in 1961.
Portugal's centuries-long influence remains visible in local architecture, particularly the many churches. Many people in Goa have Portuguese-origin surnames.
Unlike in most of India, many Goans prefer football to cricket -- and many support Portugal in international tournaments such as the World Cup.
"I follow (Portugal) too but when we have our own players we cannot put up a statue of someone from outside," Fernandes said.
It is not the first time a statue of Ronaldo, 36, has caused an upset.