Messi broke Batistuta's record of 54 goals for Argentina at the Copa America Centenario last year, and has since moved seven clear.
The duo are well ahead of Sergio Aguero and Hernan Crespo, with the Manchester City star netting his 35th in Argentina's 1-0 friendly win over Russia on Sunday (AEDT).
Batistuta said he was frustrated to have Messi break his mark, but he paid tribute to the Barcelona superstar.
"Did it annoy me that Messi took the record? A little, yes," he told Telefe.
"It was a title that I held. It's not just any old thing. You go around the world and people say, 'He's the top scorer for the Argentina national team'.
"I think I got to 54 or something like that. Lionel has more and will get almost double what I did.
"But the advantage I have is that I'm second to an extraterrestrial."
Batistuta won two Copa America titles and a Confederations Cup with Argentina, while a senior success with the national team may be about all that is missing for Messi.