Barcelona's Messi scored his 87th and 88th goals of the year in Wednesday's Copa del Rey last-16 first leg at Cordoba having thought he had broken Gerd Mueller's 1972 record of 85 on Sunday.
"We are upset. Messi still hasn't passed the milestone," Bruno Lucena, head of Flamengo's research and statistics department, told Brazilian sports daily Lance.
Lucena calculated that Zico scored 81 goals for Flamengo in 1979, plus another seven for Brazil and one in a friendly between Argentina and a Rest of the World XI.
He added that Zico missed two months of the season through injury between September and November.
"If he had played for the whole year, he would have scored more than 100 goals," he said.
Lance produced a list of goals scored by Zico in 1979. According to the statistics, he hit six goals in a game on two occasions, four goals in a game once and five hat-tricks.