The 25-year-old forward reached another milestone in his phenomenal career with a La Liga double in Sunday's 2-1 win at Real Betis, beating former West Germany striker Muller's 1972 tally of 85.
"I hope he scores a few more in the remaining matches of 2012 so that his record stands for another 40 years," Muller said in a statement issued through Bayern Munich where he works as a youth coach.
Messi, who is expected to secure a fourth successive World Player of the Year award next month, has netted 74 times for Barca and 12 for Argentina this year.
He has scored 56 in La Liga, 13 in the Champions League, three in the King's Cup and two in the Spanish Super Cup and still has two league matches and one King's Cup game to play before the end of the year.
Muller hit 72 goals for Bayern and 13 for then-West Germany in 1972 and was 27 when he set his mark.
"My record has stood for 40 years - 85 goals in 60 matches," he said. "Now the world's best player, Lionel Messi, has broken it and I am happy for him.
"Messi is an unbelievable player, a giant while also being a pleasant and rather reserved professional. Messi is fantastic - he has only one fault, he does not play for FC Bayern."
