A ban on planes flying lower than 20,000 feet will remain in place in Nairobi for the duration of Mr Obama's three-day visit, it says.
Some US media have criticised the KCAA for revealing Mr Obama's travel plans.
The US issued a travel warning for Kenya in July ahead of the visit.
The global entrepreneurship summit in Nairobi this weekend, which Mr Obama is due to address, could provide "a target for terrorists", the US State Department said in a statement.
Kenyans are preparing for significant disruption after police announced major road closures in Nairobi from Friday.
Kenyan airspace will also be closed for a further 40 minutes on Sunday when President Obama leaves for neighbouring Ethiopia.
Somali Islamist group al-Shabab has staged repeated attacks on Kenya in recent years.
In April, it killed 148 people at a university in the north and in 2013, at least 67 people died when the al-Qaeda-linked group attacked Westgate shopping centre in Nairobi.
Last month, the UK lifted its warning against travelling to part of Kenya's coast, including Mombasa.