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The shooting happened sometime after 1 a.m. in the 23200 block of Tomball Parkway at a bar and grill near Spring Cypress.
According to HCSO Chief Tommy Diaz, an alleged disturbance inside the bar spilled over into the bar's parking lot.
Investigators said once all parties were outside, two off-duty deputies, said to be working extra jobs, were trying to diffuse the situation.
Gonzalez said at least one of the men involved pulled out a pistol and was ordered by one of the deputies to put down the weapon.
HCSO said the man refused and was then shot by the deputy.
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The man was transported to the hospital in critical condition.
No one else was injured.
This shooting is one of two involving Harris County deputies early Saturday.
RELATED: Deputy struck in hand after gunfire exchange with suspected car burglar in NE Harris Co., HCSO says
A deputy who had been with HCSO for six years was shot in the hand after confronting alleged car burglars in the Atascocita area just before 3 a.m. He is expected to be OK.
Officials said both shootings are under investigation.