The company has issued a software update to fix the issue and has offered to replace defective batteries.
“The factors causing the performance issues do not present a safety risk. You may continue to use your current battery,” the company said.
Reports of problems, including swollen batteries, have been circulating since the laptops were launched in 2006.
In its support notes to users, Apple says battery packs which are “visibly deformed” are among the symptoms of battery problems.
The company advises users to install the update on all “MacBook and MacBook Pro computers and extra batteries that were purchased between February 2006 and April 2007”.
If battery problems persist after the update, Apple has said users should contact their local Apple store or retailer and the firm will arrange replacement batteries free of charge.
Other symptoms of battery problems include:
The battery is not recognised
The battery will not charge and runs down quickly
In July last year the BBC News website was contacted by Apple owners who reported problems with their new laptops.
Technology professional Dave Verwer said: “I noticed my MacBook Pro would get down to 30% battery left and then shut off without warning.
“It had done this for a couple of weeks before I noticed that the battery case was swollen and coming away from the laptop casing.”
Despite the issues, the MacBook range of laptops has been very successful for Apple.
Strong sales of the machines recently helped Apple sales soar to $5.2bn in the first three months of 2007.