The South Goa district collector Monday ordered a probe after the Indian Tricolour was hoisted upside down at the district collectorate building in Margao.
Margao is located 35 km from here.
Collector N.D. Agarwal told reporters that an enquiry has been ordered into the incident.
"Police are in-charge of hoisting the flag and not the collectorate staff. But in any case, we are ordering a probe," Agarwal said.
Hoisting a flag upside down amounts to violation of the Flag Code and can attract imprisonment up to one year.
Earlier, a torn Tricolour was seen hoisted at the same building and triggered controversy.