The court found the former Beni Suef security chief, Maj. Gen. Ahmed Shawky, innocent along with a security employee, department head and 11 soldiers, al-Masry al-Youm reported Tuesday.
A source from Egypt's Public Prosecution said the verdict would be appealed.
The men were accused of being responsible for the deaths of protesters on Jan. 28, 2011, during the revolution that ousted Hosni Mubarak as Egypt's president.
At least 800 protesters were killed and thousands of others were injured during the entire uprising.
On Sunday, Egypt's Court of Cassation ordered a retrial for Mubarak, his interior minister and six of his top security deputies after prosecutors challenged verdicts clearing them of some of the charges.