Barca's Messi was credited with the new record after going better than German legend Gerd Mueller's best of 85 goals in 1972 with a first-half brace that sealed his side's 2-1 win over Real Betis on Sunday.
But Zambian researchers disagree.
"Godfrey Chitalu scored 49 goals in the league matches and 58 in cup and international matches between January 23 and December 10, 1972," local commentator Musonda Chibulu said.
"The number of goals scored during this season goes to 107."
Chibulu and fellow researcher Jerry Muchimba compiled their proof from daily newspapers Times of Zambia and the Zambia Daily Mail, as well as the national archives.
The southern African nation's football federation intends to try and get Chitalu's tally ratified by football's governing body.
"We are planning to take the evidence to FIFA," association spokesman Eric Mwanza said.
Chitalu died with the whole national football team when the airplane they were on crashed off the coast of Gabon in 1993 on the way to a World Cup qualifier in Senegal.
He was head coach at the time.
Messi's record had already been contested on Wednesday by Brazilian club Flamengo which claimed its former player Zico scored 89 goals in the 1979 season.
Messi added to his 2012 haul with a brace in Barca's Spanish Cup win over Cordoba putting the Argentine maestro on the 88 mark.