In a statement to the media, the company said the stickers were made by one of the creators on the Line Creators Market.
"Line has no intention to disparage Buddhism but we feel deeply sorry for any inconveniences that may have been caused," the statement said.
Line was launched in 2011 by the Japanese unit of South Korean Internet service provider Naver Corp after the earthquake-tsunami tragedy damaged telephone systems nationwide, forcing staff to resort to Internet-based messaging to communicate.
The app now has more than 400 million registered users, mainly in Japan and Asia, and is growing fast in other parts of the world.
Thailand marks the fourth country with official Line offices, following Japan, South Korea and Taiwan. As of May, Thailand had the second-most Line users globally with 24 million, trailing Japan's 51 million.