"Today the army is being involved in the civil conflict, which could lead to the mass deaths of civilians and soldiers," General Yuri Dumanski, deputy head of the army's general staff, told Channel 5 television in comments broadcast Friday.
"I have decided to hand in my resignation to avoid an escalation."
The Ukrainian capital has been the scene of intense clashes between protesters wanting the departure of President Viktor Yanukovych and security forces, in a dramatic escalation of a three-month protest movement that has seen at least 77 die.
Dumanski's resignation is the second shock departure to rock the army of the crisis-hit country, after Yanukovych sacked the head of the general staff Volodymyr Zamana on Wednesday without explaining the move.
Zamana was known to have publicly disagreed with Yanukovych at the start of the month when the embattled Ukrainian leader first considered imposing a state of emergency in response to the wave of anti-government protests gripping Kiev and other parts of the country.