The amusement park company did not give a reason for the change, which takes effect next year. The Wild Safari portion of the park also will end its 2012 season a month early, on Sept. 30, except for previously scheduled VIP tours, park officials said.
Park officials said details about how the animal sanctuary will operate in the future will be made public Aug. 30.
Six Flags currently lets visitors either drive their own vehicles through its 350-acre animal sanctuary or take guided bus tours.
Since opening in 1974, the Wild Safari animal park at Six Flags has had more than 10 million drive-thru visitors.
The park's president said the sanctuary's 1,200 animals will remain at Six Flags.
"Animal preservation and education has been a cornerstone of Six Flags Great Adventure since we opened our gates in 1974," John Fitzgerald, the park president, said in a written statement. "While significant changes are on our horizon, our veterinary and animal husbandry staff will continue to provide excellent care for the more than 70 species of exotic and domestic animals that live here."
Safari Director Bill Rives, also chief veterinarian, said the drive-thru park "has been an institution for many families whose first glimpse of exotic animals was with their faces pressed up against a car window. That chapter of our history is now drawing to a close."
Park spokeswoman Kristin Siebeneicher said operational changes are based on guest feedback and research, but she declined to provide any details on what led to the decision to end the drive-thru tours. She said the company does not release business data, such as number of visitors to different attractions, for individual parks.
Six Flags Entertainment Corp., based in Grand Prairie, Texas, and New York, owns and operates 19 regional theme parks and water parks, 17 in the United States and one each in Mexico City and Montreal.
Only two sites offer animal parks, and the New Jersey Six Flags has been the only one to allow drive-thru tours.
In July, Six Flags reported that net income had more than doubled companywide in the second quarter, in part due to increased attendance. Six Flags emerged from bankruptcy protection two years ago.