Cruzeiro, due to play the first leg of the final in La Plata, have asked the Brazilian Football Confederation (CBF) to raise the issue with South American body CSF, the club said on their website.
"We want an evaluation to be made with the competent organisations in Argentina... We need them to assume responsibility, (and say) whether or not conditions are right to play the match," Cruzeiro's director of football Eduardo Maluf was quoted as saying.
"Cities in Buenos Aires province are in a state of health emergency. There are no more sporting events, all have been cancelled. (Authorities) are taking decisions that leave us all very worried," he said.
"It's not enough for the vice-president of Estudiantes to give guarantees."
The Argentine club have said they can guarantee the safety of the Brazilian team and staff from contagion of the flu strain during their time in La Plata, capital of Buenos Aires province.
Maluf said Cruzeiro had already delayed their departure for La Plata until Tuesday and travelling on the day of the match was also under consideration by the club.
The CSF gave South American teams the choice as to whether they should travel to Mexico for Libertadores Cup matches earlier this year during the H1N1 outbreak there.
Uruguayan and Brazilian players refused to go and the Mexican clubs withdrew from the competition.
