The Transformers films are wildly popular in China, and Chinese companies from milk producers to banks have flocked to have their products endorsed in the latest instalment.
The Chongqing Wulong Karst Tourism Group, which runs an area of gorges and caves in southwest China where some scenes were filmed, claims it had an agreement for the logo to be shown.
It is asking Paramount Pictures and an associated Chinese company to pay more than 20 million yuan ($3.2 million) in compensation, the state-run China Daily reported.
"People who have never been to Chongqing will not know it is Wulong in the film due to their failure to show our scenic area's logo," the report quoted Li Chu, the Group's marketing manager as saying.
A member of staff at the Chongqing Third Intermediate court told AFP that Wulong had filed a lawsuit on Tuesday, but the court would not decide until next week whether it would hear the case.
But other reports have thrown doubt on the nature of the agreement between Wulong and the filmmakers.
Paramount's Chinese associate m1905.com said in a statement on its website it "regretted" that Wulong's logo had not appeared in the film, citing miscommunication.
Paramount representatives could not be reached for comment.
Transformers: Age of Extinction is the highest ever grossing film in China with box office receipts of more than $280 million so far, the Hollywood Reporter said.