During his meeting with President Jose Raul Mulino, Rubio clarified "that the status quo is not acceptable", according to the US Department of State.
The country believes that Panama is violating the agreement signed by former President Jimmy Carter, which gave Panama full control over the canal in 1999.
The US claims, among other things, that China has gained control over the important canal, which, according to both Rubio and President Donald Trump, poses a threat to the canal and US interests.
"It is unacceptable and if no immediate changes are made, the US will take necessary measures", Rubio said to Mulino, according to the Ministry of Foreign Affairs.
The President, on the other hand, says that he has proposed talks at a lower level to "dispel all the question marks Trump has about Chinese influence".
At a press conference, he also says that he does not see any threat to the canal.
I do not see that there is currently any threat to the agreement or its validity, and even less that there is a need for a military intervention to secure the canal.
Donald Trump has threatened with a military intervention to regain control over the canal, as he believes that American ships passing through it are paying "ridiculous" fees.
In his inaugural speech in January, he said:
China controls the Panama Canal, but we did not give it to China, we gave it to Panama and we will take it back.