This is an informal expression that is mostly used in American English. When you do something `on the fly’, you do it very quickly, without spending too much time thinking about it.
This is a serious matter. I don’t think you should be taking decisions on the fly. The expression has another meaning as well. It means the ability to perform a task while you are on the move.
Padma’s new cell phone enables her to check her email on the fly.
Source: “The Hindu” – Know Your English Column – Feb 26, 2008