By crouching before impact, an Agent can soften the blow by performing an acrobatic roll. Don't do this near cliff edges though.
After Master Yuzuki agrees to make use of the Dojo, talking to her once will unlock the Ninja Roll for research.
An immensely useful ability, this allows agents to negate fall damage up to a certain height, beyond that fall damage will begin to accrue as normal. The trade-off is that there is that the roll takes a second to finish, leaving the agent vulnerable. Hold down crouch as you are falling to execute it.