The mine, located in a rural area of Antioquia department, 430 kilometers (265 miles) northwest of Bogota, was previously shuttered in June last year due to failed safety tests but it continued to operate.
The government's risk management department said all nine bodies had been recovered.
Mining operations at the facility were blatantly illegal, Mauricio Cardenas, the minister for mines and energy, told Caracol Radio.
Pumps were used to lower water levels in the mine, allowing rescuers to recover the bodies, officials coordinating the recovery mission said earlier.
Some 45 miners died last year in workplace accidents in Colombia, according to official figures.
The Colombian Geologic Service (Ingeominas) on Thursday said that the mine was operating without a license and reiterated on Friday that the facility will be closed until its owner can prove that all safety standards are met.