Environment Minister Pohamba Shifeta told AFP the move comes as crocodile numbers in parts of the southern African country have grown to a point where they are no longer sustainable.
"We have targeted different areas where the crocodile population exceeds the carrying capacity and moving onto the shore where they start to attack people," Shifeta said.
The ministry had on Wednesday said in a statement that 40 crocodiles would be captured from rivers in the northeastern, wildlife-rich regions of Kavango and Zambezi -- and auctioned off.
The government said they would be sold to anyone who could prove they have suitable habitats for the crocodiles, and who have proper export papers.
"We are also looking at where the human attacks take place in conservancies and will increase their trophy quota, we might double it," said Shifeta.
The decision was based on a study of the reptile population after an increase in reports of crocodiles wading into inhabited areas, Shifeta said.
The ministry has since 2019 paid more than 2.3 million Namibian dollars ($125,000) in compensation to families affected by crocodile attacks, some of which were fatal, it said.
The sum included 14 payouts for injuries to people, as well as compensation for the loss of livestock.
Bidding for the crocodiles is set to begin on July 17 and sales will be repeated periodically to control population numbers.