Cook says Apple will stay in the country even if the EU rule against Ireland's tax agreement with the company, noting there is no "special deal" in place and that Apple is paying 12.5% on all revenue generated there.
Apple is planning to expand it's Cork campus to provide space for 1,000 additional employees by mid-2017. The expansion would boost the number of employees in Ireland to 6,000.
Addressing the EU investigation, Cook said, "I can't say for sure what they will come back with. What I do know for sure is that if the evidence and history is viewed on a fair basis, I believe strongly ... there will be no charges and so forth."
Even if the European Commission does return an adverse ruling, Apple will stay and Ireland and support the countries in appealing it.
Apple has had a presence in Cork since 1980 with staff working on manufacturing, customer care, finance and global supply chain management.
Tánaiste Joan Burton described Apple's announcement as "a vote of confidence in Cork and in Ireland".