The visit comes as US President Joe Biden's administration seeks to boost other Asian trade partners' roles in the global tech supply chain to reduce American dependence on China.
Cook travelled to Indonesia's presidential palace in Jakarta to meet Joko Widodo, the outgoing leader more popularly known as Jokowi, who has promoted a burgeoning tech sector.
"Indonesia is a very important market for us. We talked about the president's desire to see manufacturing in the country, and it's something that we will look at," he told reporters.
"I think the investment ability in Indonesia is endless. We believe in the country," he added.
"It was a dialogue about how much potential there is in the country and our commitment to the country."
The iPhone-maker announced Tuesday it will expand its developer academies in Indonesia to four with a new facility on the Hindu resort island of Bali.
Indonesia has a young, tech-savvy population with more than 100 million people under the age of 30, but Apple is dominated in the smartphone market by Google's Android, according to statistics.
Cook later met president-elect and current defence minister Prabowo Subianto, who will take the reins from Jokowi in October after his election win in February.
The pair held talks that lasted more than an hour at the defence ministry in Jakarta, according to a ministry statement.
They "discussed various matters, especially regarding collaboration between Apple and the Indonesian government", the statement said.
It said Cook had sent a letter to Prabowo last month in which he wrote: "Looking to the future, I am confident that we will be able to open up more successful cooperation between Indonesia and Apple".
Minister of Communication and Informatics Budi Arie Setiadi last month said Cook's visit could involve talks on new Apple investments in Indonesia, including a smartphone factory.
"There are all possibilities, we'll see what the approach is, because there are a lot of Apple users in Indonesia," he said, local media reported.
Apple did not respond to an AFP request for comment about Cook's plans in Indonesia.
The company is yet to open an official store in Indonesia, forcing those who want its products to buy from resale platforms.
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