The changes will see the T37 800m - currently held by McKillop after his win in London last year and in Beijing in 2008 - removed from the 2016 programme.
It leaves him with just the T37 1500m title to defend.
The Glengormley athlete tweeted his disappointment, adding: "Unfortunately I will not have the opportunity to retain my 800m title in Rio. I am deeply disappointed with this outcome."
Meanwhile sprinter Jason Smyth, of Eglinton, will be left with just the T13 100m after the 200m was axed.
It comes after the announcement was made on Tuesday that there will be 177 athletics events in Rio, seven more than London 2012, following a widespread consultation.
It includes a 22% increase in the number of women's events.
The aim of IPC Athletics was for a better spectrum of events to be offered within the programme (short, middle distance and long distance running events, jumps and throwing events) and some events were casualties of the restructuring.
Earlier this month, the IPC announced that Rio 2016 will see around 4,350 athletes compete in 526 medal events across 22 sports.